source: trunk/src/series.m @ 1109

Last change on this file since 1109 was 1108, checked in by sommeria, 3 years ago

phys_XYZ modified for angular scan

File size: 178.7 KB
Line 
1%'series': master function associated to the GUI series.m for analysis field series 
2%------------------------------------------------------------------------
3% function varargout = series(varargin)
4% associated with the GUI series.fig
5%
6%INPUT
7% param: structure with input parameters (link with the GUI uvmat)
8%      .menu_coord_str: string for the TransformName (menu for coordinate transforms)
9%      .menu_coord_val: value for TransformName (menu for coordinate transforms)
10%      .FileName: input file name
11%      .FileName_1: second input file name
12%      .list_field: menu of input fields
13%      .index_fields: chosen index
14%      .civ1=0 or 1, .interp1,  ... : input civ field type
15%
16
17%=======================================================================
18% Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
19%   http://www.legi.grenoble-inp.fr
20%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
21%
22%     This file is part of the toolbox UVMAT.
23%
24%     UVMAT is free software; you can redistribute it and/or modify
25%     it under the terms of the GNU General Public License as published
26%     by the Free Software Foundation; either version 2 of the license,
27%     or (at your option) any later version.
28%
29%     UVMAT is distributed in the hope that it will be useful,
30%     but WITHOUT ANY WARRANTY; without even the implied warranty of
31%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
32%     GNU General Public License (see LICENSE.txt) for more details.
33%=======================================================================
34
35%------------------------------------------------------------------------
36%------------------------------------------------------------------------
37%  I - MAIN FUNCTION series
38%------------------------------------------------------------------------
39%------------------------------------------------------------------------
40function varargout = series(varargin)
41
42% Begin initialization code - DO NOT EDIT
43gui_Singleton = 1;
44gui_State = struct('gui_Name',       mfilename, ...
45                   'gui_Singleton',  gui_Singleton, ...
46                   'gui_OpeningFcn', @series_OpeningFcn, ...
47                   'gui_OutputFcn',  @series_OutputFcn, ...
48                   'gui_LayoutFcn',  [] , ...
49                   'gui_Callback',   []);
50if nargin && ischar(varargin{1})
51    gui_State.gui_Callback = str2func(varargin{1});
52end
53
54if nargout
55    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
56else
57    gui_mainfcn(gui_State, varargin{:});
58end
59% End initialization code - DO NOT EDIT
60
61%--------------------------------------------------------------------------
62% --- Executes just before series is made visible.
63%--------------------------------------------------------------------------
64function series_OpeningFcn(hObject, eventdata, handles,Param)
65
66% Choose default command line output for series
67handles.output = hObject;
68% Update handles structure
69guidata(hObject, handles);
70
71%% initial settings
72% position and  size of the GUI at opening
73set(0,'Unit','points')
74ScreenSize=get(0,'ScreenSize'); % size of the current screen, in points (1/72 inch)
75Width=900; % prefered width of the GUI in points (1/72 inch)
76Height=624; % prefered height of the GUI in points (1/72 inch)
77%adjust to screen size (reduced by a min margin)
78RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height);
79if RescaleFactor>1
80    RescaleFactor=min(RescaleFactor,1);
81end
82Width=Width*RescaleFactor;
83Height=Height*RescaleFactor;
84LeftX=80*RescaleFactor; % position of the left fig side, in pixels (put to the left side, with some margin)
85LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
86set(hObject,'Units','points')
87set(hObject,'Position',[LeftX LowY Width Height])% position and size of the GUI at opening
88
89% settings of table MinIndex_j
90set(handles.MinIndex_i,'ColumnFormat',{'numeric'})
91set(handles.MinIndex_i,'ColumnEditable',false)
92set(handles.MinIndex_i,'ColumnName',{'i min'})
93set(handles.MinIndex_i,'Data',[])% initiate Data to double (not cell)
94
95% settings of table MinIndex_j
96set(handles.MinIndex_j,'ColumnFormat',{'numeric'})
97set(handles.MinIndex_j,'ColumnEditable',false)
98set(handles.MinIndex_j,'ColumnName',{'j min'})
99set(handles.MinIndex_j,'Data',[])% initiate Data to double (not cell)
100
101% settings of table MaxIndex_i
102set(handles.MaxIndex_i,'ColumnFormat',{'numeric'})
103set(handles.MaxIndex_i,'ColumnEditable',false)
104set(handles.MaxIndex_i,'ColumnName',{'i max'})
105set(handles.MaxIndex_i,'Data',[])% initiate Data to double (not cell)
106
107% settings of table MaxIndex_j
108set(handles.MaxIndex_j,'ColumnFormat',{'numeric'})
109set(handles.MaxIndex_j,'ColumnEditable',false)
110set(handles.MaxIndex_j,'ColumnName',{'j max'})
111set(handles.MaxIndex_j,'Data',[])% initiate Data to double (not cell)
112
113% settings of table PairString
114set(handles.PairString,'ColumnName',{'pairs'})
115set(handles.PairString,'ColumnEditable',false)
116set(handles.PairString,'ColumnFormat',{'char'})
117set(handles.PairString,'Data',{''})
118
119% settings of table MaskTable
120set(handles.MaskTable,'ColumnName',{'mask name'})
121set(handles.PairString,'ColumnEditable',false)
122set(handles.PairString,'ColumnFormat',{'char'})
123set(handles.PairString,'Data',{''})
124
125series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size
126set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
127set(hObject,'DeleteFcn',{@closefcn})%
128
129% check default input data
130if ~exist('Param','var')
131    Param=[]; % default
132end
133
134%% Read the parameter file series.xml, or created from series.xml.default if it does not exist
135SeriesData=[];
136[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
137xmlfile=fullfile(path_series,'series.xml');
138if ~exist(xmlfile,'file')
139    [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
140end
141if exist(xmlfile,'file')
142    SeriesData.SeriesParam=xml2struct(xmlfile);
143    if ~(isfield(SeriesData.SeriesParam,'ClusterParam')&& isfield(SeriesData.SeriesParam.ClusterParam,'LaunchCmdFcn'))
144        [success,message]=copyfile(xmlfile,fullfile(path_series,'series_old.xml'));% update the file series.xml inot correctly documented
145        delete(xmlfile);
146        [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
147    end 
148    SeriesData.SeriesParam=xml2struct(xmlfile);
149end
150
151%% list of builtin functions in the menu ActionName
152ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'}; % WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
153NbBuiltinAction=numel(ActionList);
154set(handles.Action,'UserData',NbBuiltinAction)
155path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
156[path_series,name,ext]=fileparts(which('series')); % path to the GUI series
157path_series_fct=fullfile(path_series,'series'); % path of the functions in subdirectroy 'series'
158command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ...
159            'python -c "import fluidimage"'];
160[code, ~] = system(command);
161if code==0
162    ActionExtList={'.m';'.sh';'.py (in dev.)'}; % default choice of extensions (Matlab fct .m or compiled version .sh
163else
164    ActionExtList={'.m';'.sh'};  % python options not installed
165end
166ActionPathList=cell(NbBuiltinAction,1); % initiate the cell matrix of Action fct paths
167ActionPathList(:)={path_series_fct}; % set the default path to series fcts to all list members
168RunModeList={'local';'background'}; % default choice of extensions (Matlab fct .m or compiled version .sh)
169[s,w]=system(SeriesData.SeriesParam.ClusterParam.ExistenceTest); % look for cluster system presence
170if isequal(s,0)
171    RunModeList=[RunModeList;{'cluster'}];
172    set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika
173    set(handles.num_CPUTime,'Visible','on'); % make visible button for CPU time estimate for one ref index
174    set(handles.num_CPUTime,'String','')% default CPU time undefined
175    set(handles.CPUTime_txt,'Visible','on'); % make visible button for CPU time title
176end
177set(handles.RunMode,'String',RunModeList)% display the menu of available run modes, local, background or cluster manager
178
179%% list of builtin transform functions in the menu TransformName
180TransformList={'';'sub_field';'phys';'phys_polar'}; % WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
181NbBuiltinTransform=numel(TransformList);
182path_transform_fct=fullfile(path_series,'transform_field');
183TransformPathList=cell(NbBuiltinTransform,1); % initiate the cell matrix of Action fct paths
184TransformPathList(:)={path_transform_fct}; % set the default path to series fcts to all list members
185SeriesData.TransformPath=path_transform_fct;% store the standard path for trqnsform functions (needed for compilation)
186
187%% get the user defined functions stored in the personal file uvmat_perso.mat
188dir_perso=prefdir;
189profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
190if exist(profil_perso,'file')
191    h=load (profil_perso);
192    %get the list of previous input files in the upper bar menu Open
193    if isfield(h,'MenuFile')
194        for ifile=1:min(length(h.MenuFile),5)
195            set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
196            set(handles.(['MenuFile_' num2str(ifile+5)]),'Label',h.MenuFile{ifile});
197        end
198    end
199    %get the menu of actions
200    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
201        ActionList=[ActionList;h.ActionListUser];
202        ActionPathList=[ActionPathList;h.ActionPathListUser(:,1)];
203    end
204    %get the menu of transform fct
205    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
206        TransformList=[TransformList;h.TransformListUser];
207        TransformPathList=[TransformPathList;h.TransformPathListUser];
208    end
209end
210
211%% selection of the input Action fct
212ActionCheckExist=true(size(ActionList)); % initiate the check of the path to the listed action fct
213for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
214    ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
215end
216ActionPathList=ActionPathList(ActionCheckExist,:); % suppress the menu options which are not valid anymore
217ActionList=ActionList(ActionCheckExist);
218set(handles.ActionName,'String',[ActionList;{'more...'}])
219set(handles.ActionName,'UserData',ActionPathList)
220ActionIndex=[];
221if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
222    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
223end
224if isempty(ActionIndex)
225    ActionIndex=1;
226end
227set(handles.ActionName,'Value',ActionIndex)
228set(handles.ActionPath,'String',ActionPathList{ActionIndex})
229set(handles.ActionExt,'Value',1)
230set(handles.ActionExt,'String',ActionExtList)
231
232%% selection of the input transform fct
233TransformCheckExist=true(size(TransformList));
234for ilist=NbBuiltinTransform+1:numel(TransformList)
235    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
236end
237TransformPathList=TransformPathList(TransformCheckExist);
238TransformList=TransformList(TransformCheckExist);
239set(handles.TransformName,'String',[TransformList;{'more...'}])
240set(handles.TransformName,'UserData',TransformPathList)
241TransformIndex=[];
242if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
243    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
244end
245if isempty(TransformIndex)
246    TransformIndex=1;
247end
248set(handles.TransformName,'Value',TransformIndex)
249set(handles.TransformPath,'String',TransformPathList{TransformIndex})
250   
251%% fields input initialisation
252if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
253    set(handles.FieldName,'String',Param.list_fields); % list menu fields
254    set(handles.FieldName,'Value',Param.index_fields); % selected string index
255end
256if isfield(Param,'Coordinates')
257    if isfield(Param.Coordinates,'Coord_x')
258        set(handles.Coord_x,'String',Param.Coordinates.Coord_x)
259    end
260    if isfield(Param.Coordinates,'Coord_y')
261        set(handles.Coord_y,'String',Param.Coordinates.Coord_y)
262    end
263    if isfield(Param.Coordinates,'Coord_z')
264        set(handles.Coord_z,'String',Param.Coordinates.Coord_z)
265    end
266end
267
268%% introduce the input file name(s) if defined from input Param,
269set(handles.series,'UserData',SeriesData)% initiate Userdata
270if isfield(Param,'InputFile')
271   
272    %% fill the list of input file series
273    InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
274    if isempty(find(cellfun('isempty',InputTable)==0)) % if there is no input file, do not introduce input info
275        set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
276        return
277    end
278    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
279    if isfield(Param.InputFile,'RootPath_1')
280        InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
281        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
282    end
283    set(handles.InputTable,'Data',InputTable)
284   
285    %% define the default path for the output files
286    [InputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
287    [InputPath,Experiment,ExperimentExt]=fileparts(InputPath);
288    set(handles.Device,'String',[Device DeviceExt])
289    set(handles.Experiment,'String',[Experiment ExperimentExt])
290    if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)'))
291    set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data
292    end
293
294    %update the output path if needed
295    if ~(isfield(SeriesData,'InputPath') && strcmp(SeriesData.InputPath,InputPath))
296    if get(handles.OutputPathBrowse,'Value')==1  % fix the output path in manual mode
297        OutputPathOld=get(handles.OutputPath,'String');
298        OutputPath=uigetdir(OutputPathOld,'pick a root folder for output data');
299        set(handles.OutputPath,'String',OutputPath)
300    else %reproduce the input path for output
301        set(handles.OutputPath,'String',InputPath)
302    end
303    end
304   
305    %% determine the selected reference field indices for pair display
306   
307    [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
308    if isempty(i1)
309        i1=1;
310    end
311    if isempty(i2)
312        i2=i1;
313    end
314    ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
315    % set(handles.num_ref_i,'String',num2str(ref_i));
316    if isempty(j1)
317        j1=1;
318    end
319    if isempty(j2)
320        j2=j1;
321    end
322    ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
323    SeriesData.ref_i=ref_i;
324    SeriesData.ref_j=ref_j;
325    set(handles.series,'UserData',SeriesData)
326    update_rootinfo(handles,Param.HiddenData.i1_series{1},Param.HiddenData.i2_series{1},Param.HiddenData.j1_series{1},Param.HiddenData.j2_series{1},...
327        Param.HiddenData.FileInfo{1},Param.HiddenData.MovieObject{1},1)
328    if isfield(Param,'FileName_1')
329        %         display_file_name(handles,Param,2)
330        update_rootinfo(handles,Param.HiddenData.i1_series{2},Param.HiddenData.i2_series{2},Param.HiddenData.j1_series{2},Param.HiddenData.j2_series{2},...
331            Param.HiddenData.FileInfo{2},Param.HiddenData.MovieObject{2},2)
332    end
333    %% enable field and veltype menus, in accordance with the current action
334    ActionName_Callback([],[], handles)
335   
336    %% set length of waitbar
337    displ_time(handles)
338   
339else
340    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
341end
342if isfield(Param,'incr_i')
343    set(handles.num_incr_i,'String',num2str(Param.incr_i))
344else
345    set(handles.num_incr_i,'String','1')
346end
347if isfield(Param,'incr_j')
348    set(handles.num_incr_j,'String',num2str(Param.incr_j))
349else
350    set(handles.num_incr_j,'String','1')
351end
352
353%------------------------------------------------------------------------
354% --- Outputs from this function are returned to the command line.
355function varargout = series_OutputFcn(hObject, eventdata, handles)
356%------------------------------------------------------------------------
357varargout{1} = handles.output;
358
359%------------------------------------------------------------------------
360% --- executed when closing uvmat: delete or desactivate the associated figures if exist
361function closefcn(gcbo,eventdata)
362%------------------------------------------------------------------------
363
364% delete set_object_series if detected
365hh=findobj(allchild(0),'name','view_object_series');
366if ~isempty(hh)
367    delete(hh)
368end
369hh=findobj(allchild(0),'name','edit_object_series');
370if ~isempty(hh)
371    delete(hh)
372end
373
374%delete the bowser if detected
375hh=findobj(allchild(0),'tag','browser');
376if ~isempty(hh)
377    delete(hh)
378end
379
380
381%------------------------------------------------------------------------
382%------------------------------------------------------------------------
383%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
384% automatically sets the global properties when the rootfile name is introduced
385% then activate the view-field actionname if selected
386% it is activated either by clicking on the RootPath window or by the
387% browser
388%------------------------------------------------------------------------
389%------------------------------------------------------------------------
390% --- fct activated by the browser under 'Open'
391%------------------------------------------------------------------------ 
392function MenuBrowse_Callback(hObject, eventdata, handles)
393%% look for the previously opened file 'oldfile'
394InputTable=get(handles.InputTable,'Data');
395oldfile=InputTable{1,1};
396if isempty(oldfile)
397    % use a file name stored in prefdir
398    dir_perso=prefdir;
399    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
400    if exist(profil_perso,'file')
401        h=load (profil_perso);
402        if isfield(h,'RootPath') && ischar(h.RootPath)
403            oldfile=h.RootPath;
404        end
405    end
406end
407%% launch the browser
408fileinput=uigetfile_uvmat('pick an input file in the series',oldfile);
409hh=dir(fileinput);
410if numel(hh)>1
411    msgbox_uvmat('ERROR','invalid input, probably a broken link');
412else
413    if ~isempty(fileinput)
414        display_file_name(handles,fileinput,'one')
415    end
416end
417
418% --------------------------------------------------------------------
419function MenuBrowseAppend_Callback(hObject, eventdata, handles)
420
421%% look for the previously opened file 'oldfile'
422InputTable=get(handles.InputTable,'Data');
423RootPathCell=InputTable(:,1);
424if isempty(RootPathCell{1})% no input file in the table
425     MenuBrowse_Callback(hObject, eventdata, handles)%refresh the input table, not append
426     return
427end
428SubDirCell=InputTable(:,2);
429oldfile=fullfile(RootPathCell{1},SubDirCell{1});
430
431%% use a file name stored in prefdir
432dir_perso=prefdir;
433profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
434if exist(profil_perso,'file')
435    h=load (profil_perso);
436    if isfield(h,'RootPath') && ischar(h.RootPath)
437        oldfile=h.RootPath;
438    end
439end
440
441%% launch the browser
442fileinput=uigetfile_uvmat('pick a file to append in the input table',oldfile);
443hh=dir(fileinput);
444if numel(hh)>1
445    msgbox_uvmat('ERROR','invalid input, probably a broken link');
446else
447    if ~isempty(fileinput)
448        display_file_name(handles,fileinput,'append')
449    end
450end
451
452%------------------------------------------------------------------------
453% --- fct activated by selecting a previous file under the menu Open
454%------------------------------------------------------------------------
455function MenuFile_Callback(hObject, eventdata, handles)
456
457errormsg=display_file_name(handles,get(hObject,'Label'),'one');
458if ~isempty(errormsg)
459    set(hObject,'Label','')
460    MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
461        {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
462    str_find=strcmp(get(hObject,'Label'),MenuFile);
463    MenuFile(str_find)=[]; % suppress the input file to the list
464    for ifile=1:numel(MenuFile)
465        set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
466    end
467end
468
469%------------------------------------------------------------------------
470% --- fct activated by selecting a previous file under the menu Open/append
471%------------------------------------------------------------------------
472function MenuFile_append_Callback(hObject, eventdata, handles)
473
474InputTable=get(handles.InputTable,'Data');
475if isempty(InputTable{1,1})% no input file in the table
476    display_file_name(handles,get(hObject,'Label'),'one') %refresh the input table, not append
477else
478    display_file_name(handles,get(hObject,'Label'),'append')% append the selected file to the current list of InputTable
479end
480
481%------------------------------------------------------------------------
482% --- fct activated by the browser under 'Open campaign/Browse...'
483%------------------------------------------------------------------------
484function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
485
486%% look for the previously opened file 'oldfile'
487InputTable=get(handles.InputTable,'Data');
488if ~isempty(InputTable)
489oldfile=[InputTable{1,1} InputTable{1,2}];
490else
491    % use a file name stored in prefdir
492    dir_perso=prefdir;
493    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
494    if exist(profil_perso,'file')
495        h=load (profil_perso);
496        if isfield(h,'MenuCampaign') && ~isempty(h.MenuCampaign)&& ischar(h.MenuCampaign{1})
497            oldfile=h.MenuCampaign{1};
498        end
499    end
500end
501InputTable{1,1}='...';
502set(handles.InputTable,'Data',InputTable)
503browse_data(oldfile,'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
504% NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
505% icount=0;
506% for iexp=1:numel(OutPut.Experiment)
507%     for idevice=1:numel(OutPut.DataSeries)
508%         icount=icount+1;
509%         InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
510%         InputTable{icount,2}=OutPut.DataSeries{idevice};
511%         if isempty(InputTable{icount,3})
512%             if icount>1
513%             InputTable{icount,3}=InputTable{icount-1,3};
514%             else
515%                 InputTable{icount,3}='';
516%             end
517%         end
518%         if isempty(InputTable{icount,4})
519%             if icount>1
520%             InputTable{icount,4}=InputTable{icount-1,4};
521%             else
522%                 InputTable{icount,4}='';
523%             end
524%         end
525%                 if isempty(InputTable{icount,5})
526%             if icount>1
527%             InputTable{icount,5}=InputTable{icount-1,5};
528%             else
529%                 InputTable{icount,5}='';
530%             end
531%         end
532%     end
533% end
534% if size(InputTable,1)>icount
535%     InputTable(icount+1:size(InputTable,1),:)=[];
536% end
537%REFRESH_Callback(hObject, eventdata, handles)
538
539% --------------------------------------------------------------------
540% function MenuCampaign_Callback(hObject, eventdata, handles)
541% % --------------------------------------------------------------------
542%
543% OutPut=browse_data(get(hObject,'Label'),'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
544% if ~isfield(OutPut,'Campaign')
545%     return
546% end
547% NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
548% icount=0;
549% InputTable=get(handles.InputTable,'Data');
550% for iexp=1:numel(OutPut.Experiment)
551%     for idevice=1:numel(OutPut.DataSeries)
552%         icount=icount+1;
553%         InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
554%         InputTable{icount,2}=OutPut.DataSeries{idevice};
555%         if isempty(InputTable{icount,3})
556%             if icount>1
557%                 InputTable{icount,3}=InputTable{icount-1,3};
558%             else
559%                 InputTable{icount,3}='';
560%             end
561%         end
562%         if isempty(InputTable{icount,4})
563%             if icount>1
564%                 InputTable{icount,4}=InputTable{icount-1,4};
565%             else
566%                 InputTable{icount,4}='';
567%             end
568%         end
569%         if isempty(InputTable{icount,5})
570%             if icount>1
571%                 InputTable{icount,5}=InputTable{icount-1,5};
572%             else
573%                 InputTable{icount,5}='';
574%             end
575%         end
576%     end
577% end
578% if size(InputTable,1)>icount
579%     InputTable(icount+1:size(InputTable,1),:)=[];
580% end
581% set(handles.InputTable,'Data',InputTable)
582% REFRESH_Callback(hObject, eventdata, handles)
583
584
585% --- Executes when selected cell(s) is changed in InputTable.
586function InputTable_CellSelectionCallback(hObject, eventdata, handles)
587iline=[];
588if ~isempty(eventdata.Indices)
589    iline=eventdata.Indices(1);
590end
591set(handles.InputLine,'String',num2str(iline));
592
593%------------------------------------------------------------------------
594% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
595%------------------------------------------------------------------------
596function InputTable_KeyPressFcn(hObject, eventdata, handles)
597set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
598set(handles.OutputSubDir,'BackgroundColor',[1 0 1])% set edit box OutputSubDir to magenta color to indicate that refresh may be needed
599xx=double(get(handles.series,'CurrentCharacter')); % get the keyboard character
600if ~isempty(xx)
601    switch xx
602        case 31 %downward arrow
603            InputTable=get(handles.InputTable,'Data');
604            iline=str2double(get(handles.InputLine,'String'));
605            if isequal(iline,size(InputTable,1))% arrow downward
606                InputTable=[InputTable;InputTable(iline,:)]; % create a new line as a copy of the last one
607                set(handles.InputTable,'Data',InputTable);
608            end
609        case 127  %key 'Suppress'
610            ClearLine_Callback(hObject, eventdata, handles)
611    end
612end
613
614%------------------------------------------------------------------------
615% --- Executes on button press in REFRESH.
616function REFRESH_Callback(hObject, eventdata, handles)
617%------------------------------------------------------------------------
618check_input_file_series(handles)
619
620%% enable field and veltype menus, in accordance with the current action
621ActionInput_Callback([],[], handles)
622
623
624function check_input_file_series(handles)
625InputTable=get(handles.InputTable,'Data');
626set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
627set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
628drawnow
629empty_line=false(size(InputTable,1),1);
630for iline=1:size(InputTable,1)
631    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));
632end
633if ~isempty(find(empty_line,1))
634    InputTable(empty_line,:)=[]; % remove empty lines
635    set(handles.InputTable,'Data',InputTable)
636    ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
637    for ilist=1:numel(ListTable)
638        Table=get(handles.(ListTable{ilist}),'Data');
639        Table(empty_line,:)=[]; % remove empty lines
640        set(handles.(ListTable{ilist}),'Data',Table);
641    end
642    set(handles.series,'UserData',[])%refresh the stored info
643end
644nbview=size(InputTable,1);
645for iview=1:nbview
646    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
647    if ~exist(RootPath,'dir')
648        i1_series=[];
649        RootFile='';
650    else %scan the input folder
651        InputTable{iview,3}=regexprep(InputTable{iview,3},'^/','');
652            [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=...
653                find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
654    end
655    % if no file is found, open a browser
656    if isempty(RootFile)&& isempty(i1_series)
657        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
658        if isempty(fileinput)
659            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
660            return
661        else
662            display_file_name(handles,fileinput,iview)
663        end
664    else
665       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
666    end
667end
668
669%% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
670MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
671set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
672MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
673set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
674MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
675
676set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
677MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
678set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
679PairString=get(handles.PairString,'Data'); % retrieve the min indices in the table MinIndex
680set(handles.PairString,'Data',PairString(1:nbview,:));
681TimeTable=get(handles.TimeTable,'Data'); % retrieve the min indices in the table MinIndex
682set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
683
684%% set length of waitbar
685displ_time(handles)
686set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
687set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
688
689
690
691%------------------------------------------------------------------------
692% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
693%------------------------------------------------------------------------
694% INPUT:
695% handles: handles of elements in the GUI
696% Param: structure of input parameters, including  input file name and path
697% iview: line index in the input table
698%       or 'one': refresh the list
699%         'append': add a new line to the input table
700function errormsg=display_file_name(handles,Param,iview)
701 
702set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
703drawnow
704errormsg=''; % default
705if ischar(Param)
706    fileinput=Param;
707else% input set when series is opened (called by the GUI uvmat)
708    fileinput=Param.FileName;
709end
710   
711%% get the input root name, indices, file extension and nomenclature NomType
712if isempty(regexp(fileinput,'^http')) && ~exist(fileinput,'file')
713    errormsg=['input file ' fileinput  ' does not exist'];
714    msgbox_uvmat('ERROR',errormsg)
715    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
716    return
717end
718
719%% detect root name, nomenclature and indices in the input file name:
720[FilePath,FileName,FileExt]=fileparts(fileinput);
721%%%%%%%%%%%%%%%%%%
722%TODO: case of input by uvmat: do not check agai the input seies %%%%%%%
723%%%%%%%%%%%%%%%%%%%
724% detect the file type, get the movie object if relevant, and look for the corresponding file series:
725% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
726[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
727FileType=FileInfo.FileType;
728if isempty(RootFile)&&isempty(i1_series)
729    errormsg='no input file in the series';
730    msgbox_uvmat('ERROR',errormsg)
731    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
732    return
733end
734if strcmp(FileType,'txt')
735    edit(fileinput)
736    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
737    return
738elseif strcmp(FileType,'xml')
739    editxml(fileinput)
740    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
741     return
742elseif strcmp(FileType,'figure')
743    open(fileinput)
744    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
745     return
746end
747
748%% enable other menus and uicontrols
749set(handles.RUN, 'Enable','On')
750set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
751set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
752drawnow
753
754
755%% fill the list of file series
756InputTable=get(handles.InputTable,'Data');
757SeriesData=get(handles.series,'UserData');
758
759if strcmp(iview,'append') % display the input data as a new line in the table
760    iview=size(InputTable,1)+1; % the next line in InputTable becomes the current line
761elseif strcmp(iview,'one') % refresh the list of  input  file series
762    iview=1; % the first line in InputTable becomes the current line
763    InputTable={'','','','',''};
764    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
765    set(handles.MinIndex_i,'Data',[])
766    set(handles.MaxIndex_i,'Data',[])
767    set(handles.MinIndex_j,'Data',[])
768    set(handles.MaxIndex_j,'Data',[])
769    set(handles.PairString,'Data',{''})
770    SeriesData.CheckPair=0; % reset the list of input lines with pairs
771    SeriesData.i1_series={};
772    SeriesData.i2_series={};
773    SeriesData.j1_series={};
774    SeriesData.j2_series={};
775    SeriesData.FileType={};
776    SeriesData.FileInfo={};
777    SeriesData.Time={};
778end
779if isfield(SeriesData,'i1_series')
780    SeriesData.i1_series(iview+1:end)=[];
781    SeriesData.i2_series(iview+1:end)=[];
782    SeriesData.j1_series(iview+1:end)=[];
783    SeriesData.j2_series(iview+1:end)=[];
784    SeriesData.FileType(iview+1:end)=[];
785    SeriesData.FileInfo(iview+1:end)=[];
786    SeriesData.Time(iview+1:end)=[];
787end
788InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
789if iview >1
790    set(handles.InputLine,'String',num2str(iview))
791end
792set(handles.InputTable,'Data',InputTable)
793
794%% determine the selected reference field indices for pair display
795if isempty(i1)
796    i1=1;
797end
798if isempty(i2)
799    i2=i1;
800end
801ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
802% set(handles.num_ref_i,'String',num2str(ref_i));
803if isempty(j1)
804    j1=1;
805end
806if isempty(j2)
807    j2=j1;
808end
809ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
810SeriesData.ref_i=ref_i;
811SeriesData.ref_j=ref_j;
812
813%% update first and last indices if they do not exist
814Param=read_GUI(handles.series);
815first_j=[];
816if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
817last_j=[];
818if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
819PairString='';
820if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
821[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
822FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
823    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
824if ~exist(FirstFileName,'file')
825    set(handles.num_first_i,'String',num2str(ref_i))
826    set(handles.num_first_j,'String',num2str(ref_j))
827end
828[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
829LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
830    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
831if ~exist(LastFileName,'file')
832    set(handles.num_last_i,'String',num2str(ref_i))
833    set(handles.num_last_j,'String',num2str(ref_j))
834end
835
836%% update the list of recent files in the menubar and save it for future opening
837MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
838    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
839str_find=strcmp(fileinput,MenuFile);
840if isempty(find(str_find,1))
841    MenuFile=[{fileinput};MenuFile]; % insert the current file if not already in the list
842end
843for ifile=1:min(length(MenuFile),5)
844    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
845end
846dir_perso=prefdir;
847profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
848if exist(profil_perso,'file')
849    save (profil_perso,'MenuFile','-append'); % store the file names for future opening of uvmat
850else
851    save (profil_perso,'MenuFile','-V6'); % store the file names for future opening of uvmat
852end
853% save the opened file to initiate future opening
854SeriesData.RefFile{iview}=fileinput; % reference opening file for line iview
855SeriesData.Ref_i1=i1;
856SeriesData.Ref_i2=i2;
857SeriesData.Ref_j1=j1;
858SeriesData.Ref_j2=j2;
859
860%% define the path for the output files
861[InputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
862[InputPath,Experiment,ExperimentExt]=fileparts(InputPath);
863set(handles.Device,'String',[Device DeviceExt])
864set(handles.Experiment,'String',[Experiment ExperimentExt])
865if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)'))
866    set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data
867end
868
869%update the output path if needed
870if ~(isfield(SeriesData,'InputPath') && strcmp(SeriesData.InputPath,InputPath))
871    if get(handles.OutputPathBrowse,'Value')==1  % fix the output path in manual mode
872        OutputPathOld=get(handles.OutputPath,'String');
873        OutputPath=uigetdir(OutputPathOld,'pick a root folder for output data');
874        set(handles.OutputPath,'String',OutputPath)
875    else %reproduce the input path for output
876        set(handles.OutputPath,'String',InputPath)
877    end
878    SeriesData.InputPath=InputPath;
879end
880
881set(handles.series,'UserData',SeriesData)
882
883set(handles.InputTable,'BackgroundColor',[1 1 1])
884
885%% initiate input file series and refresh the current field view:     
886update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
887%% enable field and veltype menus, in accordance with the current action
888ActionName_Callback([],[], handles)
889
890%% set length of waitbar
891displ_time(handles)
892
893set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)
894
895%------------------------------------------------------------------------
896% --- Update information about a new field series (indices to scan, timing,
897%     calibration from an xml file
898function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
899%------------------------------------------------------------------------
900InputTable=get(handles.InputTable,'Data');
901
902%% display the min and max indices for the whole file series
903if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
904    MinIndex_j=1; % index j set to 1 by default
905    MaxIndex_j=1;
906    MinIndex_i=find(i1_series(1,2,:), 1 )-1; % min ref index i detected in the series (corresponding to the first non-zero value of i1_series, except for zero index)
907    MaxIndex_i=find(i1_series(1,2,:),1,'last' )-1; % max ref index i detected in the series (corresponding to the last non-zero value of i1_series)
908else
909    ref_i=squeeze(max(i1_series(1,:,:),[],2)); % select ref_j index for each ref_i
910    ref_j=squeeze(max(j1_series(1,:,:),[],3)); % select ref_i index for each ref_j
911     MinIndex_i=min(find(ref_i))-1;
912     MaxIndex_i=max(find(ref_i))-1;
913     MaxIndex_j=max(find(ref_j))-1;
914     MinIndex_j=min(find(ref_j))-1;
915    diff_j_max=diff(ref_j);
916    diff_i_max=diff(ref_i);
917    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
918        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
919    end
920    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
921        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
922    end
923end
924if isequal(MinIndex_i,-1)
925    MinIndex_i=0;
926end
927if isequal(MinIndex_j,-1)
928    MinIndex_j=0;
929end
930MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
931MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
932MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
933MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
934if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
935    MinIndex_i_table(iview,1)=MinIndex_i;
936    MaxIndex_i_table(iview,1)=MaxIndex_i;
937end
938if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
939    MinIndex_j_table(iview,1)=MinIndex_j;
940    MaxIndex_j_table(iview,1)=MaxIndex_j;
941end
942set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
943set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
944set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
945set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
946SeriesData=get(handles.series,'UserData');
947
948%% adjust the first and last indices for the selected series, only if requested by the bounds
949% i index, compare input to min index i
950first_i=str2num(get(handles.num_first_i,'String')); % retrieve previous first i
951% ref_i=str2num(get(handles.num_ref_i,'String')); % index i given by the input field
952ref_i=1;
953if isfield(SeriesData,'ref_i')
954    ref_i=SeriesData.ref_i;
955end
956if isempty(first_i)
957    first_i=ref_i; % first_i updated by the input value
958elseif first_i < MinIndex_i
959    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
960elseif first_i >MaxIndex_i
961    first_i=MaxIndex_i; % first_i set to the max i index (restricted by oter input lines)
962end
963% j index,  compare input to min index j
964first_j=str2num(get(handles.num_first_j,'String'));
965ref_j=1;
966if isfield(SeriesData,'ref_j')
967    ref_j=SeriesData.ref_j;
968end
969if isempty(first_j)
970    first_j=ref_j; % first_j updated by the input value
971elseif first_j<MinIndex_j
972    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
973elseif first_j >MaxIndex_j
974    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
975end
976% i index, compare input to max index i
977last_i=str2num(get(handles.num_last_i,'String'));
978if isempty(last_i)
979    last_i=ref_i;
980elseif last_i > MaxIndex_i
981    last_i=MaxIndex_i;
982elseif last_i<first_i
983    last_i=first_i;
984end
985% j index, compare input to max index j
986last_j=str2num(get(handles.num_last_j,'String'));
987if isempty(last_j)
988    last_j=ref_j;
989elseif last_j>MaxIndex_j
990    last_j=MaxIndex_j;
991elseif last_j<first_j
992    last_j=first_j;
993end
994set(handles.num_first_i,'String',num2str(first_i));
995set(handles.num_first_j,'String',num2str(first_j));
996set(handles.num_last_i,'String',num2str(last_i));
997set(handles.num_last_j,'String',num2str(last_j));
998
999%% number of slices set by default
1000NbSlice=[]; % default
1001% read  value set by the first series for the append mode (iwiew >1)
1002if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
1003    NbSlice=str2double(get(handles.num_NbSlice,'String'));
1004end
1005
1006%% default time settings
1007TimeUnit='';
1008% read  value set by the first series for the append mode (iwiew >1)
1009if iview>1
1010    TimeUnit=get(handles.TimeUnit,'String');
1011end
1012TimeName='';
1013Time=[]; % default
1014TimeMin=[];
1015TimeFirst=[];
1016TimeLast=[];
1017TimeMax=[];
1018
1019%%  read image documentation file if found
1020XmlData=[];
1021check_calib=0;
1022XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
1023if ~isempty(XmlFileName)
1024    [XmlData,errormsg]=imadoc2struct(XmlFileName);
1025    if ~isempty(errormsg)
1026        msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
1027    end
1028    % read time if available
1029    if isfield(XmlData,'Time')
1030        Time=XmlData.Time;
1031        TimeName='xml';
1032    end
1033    if isfield(XmlData,'Camera')
1034        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1035            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
1036                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
1037            end
1038            TimeUnit=XmlData.Camera.TimeUnit;
1039        end
1040    end
1041    % number of slices
1042    if isfield(XmlData,'TranslationMotor')&& isfield(XmlData.TranslationMotor,'NbSlice')
1043        NbSlice_motor=XmlData.TranslationMotor.NbSlice;
1044        if ~isempty(NbSlice) && ~isequal(NbSlice_motor,NbSlice)
1045                msgbox_uvmat('WARNING','inconsistent Z numbers of Z indices');
1046        else
1047            NbSlice=NbSlice_motor;
1048        end
1049    end
1050end
1051if ~isempty(NbSlice)
1052set(handles.num_NbSlice,'String',num2str(NbSlice))
1053set(handles.num_NbSlice,'Visible','on')
1054end
1055
1056%% read timing  from the current file (prioritary)
1057if ~isempty(VideoObject)% case of movies
1058    imainfo=get(VideoObject);
1059    if isfield(imainfo,'NumFrames')
1060        imainfo.NumberOfFrames=imainfo.NumFrames;
1061    end
1062    if isempty(j1_series) % frame index along i
1063        Time=zeros(imainfo.NumberOfFrames+1,2);
1064        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
1065    else
1066        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
1067    end
1068    TimeName='video';
1069end
1070
1071
1072%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
1073if ~isempty(TimeName)
1074    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
1075    if size(Time)>=[first_i+1 first_j+1]
1076        TimeFirst=Time(first_i+1,first_j+1);
1077    end
1078    if size(Time)>=[last_i+1 last_j+1]
1079        TimeLast=Time(last_i+1,last_j+1);
1080    end
1081    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1]
1082        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
1083    end
1084end
1085
1086%% update the time table
1087TimeTable=get(handles.TimeTable,'Data');
1088TimeTable{iview,1}=TimeName;
1089TimeTable{iview,2}=TimeMin;
1090TimeTable{iview,3}=TimeFirst;
1091TimeTable{iview,4}=TimeLast;
1092TimeTable{iview,5}=TimeMax;
1093set(handles.TimeTable,'Data',TimeTable)
1094
1095%% update the series info in 'UserData'
1096SeriesData.i1_series{iview}=i1_series;
1097SeriesData.i2_series{iview}=i2_series;
1098SeriesData.j1_series{iview}=j1_series;
1099SeriesData.j2_series{iview}=j2_series;
1100SeriesData.FileType{iview}=FileInfo.FileType;
1101SeriesData.FileInfo{iview}=FileInfo;
1102SeriesData.Time{iview}=Time;
1103
1104SeriesData.TimeName=TimeName;
1105
1106if check_calib
1107    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
1108end
1109set(handles.series,'UserData',SeriesData)
1110
1111%% update pair menus
1112hset_pair=findobj(allchild(0),'Tag','set_pairs');
1113if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
1114CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
1115PairString=get(handles.PairString,'Data');
1116if CheckPair% if pairs need to be display for line iview
1117    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
1118    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
1119    PairString{iview,1}=Menu{1};
1120else
1121    PairString{iview,1}=''; % no pair for #iview
1122end
1123set(handles.PairString,'Data',PairString)
1124if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
1125    set(handles.PairString,'Visible','off')
1126    set(handles.SetPairs,'Visible','off')
1127else
1128    set(handles.PairString,'Visible','on')
1129    set(handles.SetPairs,'Visible','on')
1130end
1131
1132
1133%% display the set of existing files as an image
1134set(handles.FileStatus,'Units','pixels')
1135Position=get(handles.FileStatus,'Position');
1136set(handles.FileStatus,'Units','normalized')
1137%xI=0.5:Position(3)-0.5;
1138nbview=numel(SeriesData.i1_series);
1139j_max=cell(1,nbview);
1140MaxIndex_i=ones(1,nbview); % default
1141MinIndex_i=ones(1,nbview); % default
1142for iline=1:nbview
1143    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); % max on pair index
1144    j_max{iline}=max(pair_max,[],1); % max on j index
1145    if ~isempty(j_max{iline})
1146    MaxIndex_i(iline)=find(j_max{iline}, 1, 'last' )-1; % max ref index i
1147    MinIndex_i(iline)=find(j_max{iline}, 1 )-1; % min ref index i
1148    end
1149end
1150MinIndex_i=min(MinIndex_i);
1151MaxIndex_i=max(MaxIndex_i);
1152range_index=MaxIndex_i-MinIndex_i+1;
1153range_y=max(1,floor(Position(4)/nbview));
1154npx=floor(Position(3));
1155file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
1156CData=zeros(nbview*range_y,npx); % initiate the image representing the existing files
1157for iline=1:nbview
1158    ind_y=1+(iline-1)*range_y:iline*range_y;
1159    LineData=zeros(size(file_indices));
1160    file_select=file_indices(file_indices<=numel(j_max{iline}));
1161    ind_select=file_indices<=numel(j_max{iline});
1162    LineData(ind_select)=j_max{iline}(file_select)~=0;
1163    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1164end
1165CData=cat(3,zeros(size(CData)),CData,zeros(size(CData))); % make color images r=0,g,b=0
1166set(handles.FileStatus,'CData',CData);
1167
1168%-----------------------------------------------------------guide -------------
1169%------------------------------------------------------------------------
1170%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1171%------------------------------------------------------------------------
1172
1173
1174% ---- determine the menu to put in mode and advice a default choice
1175%------------------------------------------------------------------------
1176function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1177%------------------------------------------------------------------------   
1178ModeMenu={''};
1179if isempty(j2_series)% no j pair
1180    ModeValue=1;
1181    if ~isempty(i2_series)
1182        ModeMenu={'series(Di)'}; % pair menu with only option Di
1183    end
1184else %existence of j pairs
1185    pair_max=squeeze(max(i1_series,[],1)); % max on pair index
1186    j_max=max(pair_max,[],1);
1187    MaxIndex_i=find(j_max, 1, 'last' )-1; % max ref index i
1188    MinIndex_i=find(j_max, 1 )-1; % min ref index i
1189    i_max=max(pair_max,[],2);
1190    MaxIndex_j=find(i_max, 1, 'last' )-1; % max ref index i
1191    MinIndex_j=find(i_max, 1 )-1; % min ref index i
1192    if MaxIndex_j==MinIndex_j
1193        ModeValue=1;
1194        ModeMenu={'bursts'};
1195    elseif MaxIndex_i==MinIndex_i
1196        ModeValue=1;
1197        ModeMenu={'series(Dj)'};
1198    else
1199        ModeMenu={'bursts';'series(Dj)'};
1200        if (MaxIndex_j-MinIndex_j)>10
1201            ModeValue=2; % set mode to series(Dj) if more than 10 j values
1202        else
1203            ModeValue=1;
1204        end
1205    end
1206end
1207
1208
1209%------------------------------------------------------------------------
1210%fill the menu of possible pairs as input
1211function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1212%------------------------------------------------------------------------
1213displ_pair={};
1214if isempty(TimeUnit)
1215    dtunit='e-03';
1216else
1217    dtunit=['m' TimeUnit];
1218end
1219switch mode
1220    case 'series(Di)'
1221        diff_i=i2_series-i1_series;
1222        min_diff=min(diff_i(diff_i>0));
1223        max_diff=max(diff_i(diff_i>0));
1224        for ipair=min_diff:max_diff
1225            if ~isempty(find(diff_i==ipair,1))% if the considered difference exists as input
1226                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1227                if size(time,1)>=ref_i+ceil(ipair/2)
1228                    if ref_i<=floor(ipair/2)
1229                        ref_i=floor(ipair/2)+1; % shift ref_i to get the first pair
1230                    end
1231                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1232                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1233                end
1234                displ_pair=[displ_pair;{pair_string}];
1235            end
1236        end
1237        if ~isempty(displ_pair)
1238            displ_pair=[displ_pair;{'Di=*|*'}];
1239        end
1240    case 'series(Dj)'
1241        if isempty(j2_series)
1242            msgbox_uvmat('ERROR','no j1-j2 pair available')
1243            return
1244        end
1245        diff_j=j2_series-j1_series;
1246        min_diff=min(diff_j(diff_j>0));
1247        max_diff=max(diff_j(diff_j>0));
1248        for ipair=min_diff:max_diff
1249            if numel(diff_j(diff_j==ipair))>0
1250                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1251                if ~isempty(time)
1252                    if ref_j<=floor(ipair/2)
1253                        ref_j=floor(ipair/2)+1; % shift ref_i to get the first pair
1254                    end
1255                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1256                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1257                end
1258                displ_pair=[displ_pair;{pair_string}];
1259            end
1260        end
1261        if ~isempty(displ_pair)
1262            displ_pair=[displ_pair;{'Dj=*|*'}];
1263        end
1264    case 'bursts'
1265        if isempty(j2_series)
1266            msgbox_uvmat('ERROR','no j1-j2 pair available')
1267            return
1268        end
1269        %diff_j=j2_series-j1_series;
1270        min_j1=min(j1_series(j1_series>0));
1271        max_j1=max(j1_series(j1_series>0));
1272        min_j2=min(j2_series(j2_series>0));
1273        max_j2=max(j2_series(j2_series>0));
1274        for pair1=min_j1:min(max_j1,min_j1+20)
1275            for pair2=min_j2:min(max_j2,min_j2+20)
1276                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1277                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1278                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1279                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1280                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1281                    displ_pair=[displ_pair;{pair_string}];
1282                end
1283            end
1284        end
1285        if ~isempty(displ_pair)
1286            displ_pair=[displ_pair;{'j=*-*'}];
1287        end
1288end
1289
1290%------------------------------------------------------------------------
1291function num_first_i_Callback(hObject, eventdata, handles)
1292%------------------------------------------------------------------------
1293num_last_i_Callback(hObject, eventdata, handles)
1294
1295%------------------------------------------------------------------------
1296function num_last_i_Callback(hObject, eventdata, handles)
1297%------------------------------------------------------------------------
1298SeriesData=get(handles.series,'UserData');
1299if ~isfield(SeriesData,'Time')
1300    SeriesData.Time{1}=[];
1301end
1302displ_time(handles);
1303
1304%------------------------------------------------------------------------
1305function num_first_j_Callback(hObject, eventdata, handles)
1306%------------------------------------------------------------------------
1307 num_last_j_Callback(hObject, eventdata, handles)
1308
1309%------------------------------------------------------------------------
1310function num_last_j_Callback(hObject, eventdata, handles)
1311%------------------------------------------------------------------------
1312% first_j=str2num(get(handles.num_first_j,'String'));
1313% last_j=str2num(get(handles.num_last_j,'String'));
1314% ref_j=ceil((first_j+last_j)/2);
1315% set(handles.num_ref_j,'String', num2str(ref_j))
1316% num_ref_j_Callback(hObject, eventdata, handles)
1317SeriesData=get(handles.series,'UserData');
1318if ~isfield(SeriesData,'Time')
1319    SeriesData.Time{1}=[];
1320end
1321displ_time(handles);
1322
1323%------------------------------------------------------------------------
1324% ---- find the times corresponding to the first and last indices of a series
1325function displ_time(handles)
1326%------------------------------------------------------------------------
1327SeriesData=get(handles.series,'UserData'); %
1328if ~isfield(SeriesData,'Time')
1329    return
1330end
1331PairString=get(handles.PairString,'Data');
1332ref_i_1=str2num(get(handles.num_first_i,'String')); % first reference index
1333ref_i_2=str2num(get(handles.num_last_i,'String')); % last reference index
1334ref_j_1=[];ref_j_2=[];
1335if strcmp(get(handles.num_first_j,'Visible'),'on')
1336ref_j_1=str2num(get(handles.num_first_j,'String'));
1337ref_j_2=str2num(get(handles.num_last_j,'String'));
1338end
1339[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1340[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1341TimeTable=get(handles.TimeTable,'Data');
1342%%%%%%
1343%TODO: read time in netcdf file, see ActionName_Callback
1344%%%%%%%
1345%Pairs=get(handles.PairString,'Data');
1346for iview=1:size(TimeTable,1)
1347    if size(SeriesData.Time,1)<iview
1348        break
1349    end
1350    TimeTable{iview,3}=[];
1351    TimeTable{iview,4}=[];
1352    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1353        if isempty(ref_j_1)
1354            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1355            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1356        else
1357            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1358            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1359        end
1360        TimeTable{iview,3}=time_first; % TODO: take into account pairs
1361        TimeTable{iview,4}=time_last; % TODO: take into account pairs
1362    end
1363end
1364set(handles.TimeTable,'Data',TimeTable)
1365
1366%% set the waitbar position with respect to the min and max in the series
1367MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1368MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1369pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1370pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1371if isempty(pos_first), pos_first=0; end
1372if isempty(pos_last), pos_last=1; end
1373Position=get(handles.Waitbar,'Position'); % position of the waitbar:= [ x,y, width, height]
1374Position_status=get(handles.FileStatus,'Position');
1375Position(1)=Position_status(1)+Position_status(3)*pos_first;
1376Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001); % width must remain positive
1377set(handles.Waitbar,'Position',Position)
1378update_waitbar(handles.Waitbar,0)
1379
1380%------------------------------------------------------------------------
1381% --- Executes when selected cell(s) is changed in PairString.
1382function PairString_CellSelectionCallback(hObject, eventdata, handles)
1383%------------------------------------------------------------------------   
1384if numel(eventdata.Indices)>=1
1385    PairString=get(hObject,'Data');
1386    if ~isempty(PairString{eventdata.Indices(1)})
1387        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1388    end
1389end
1390
1391%-------------------------------------
1392function enable_i(handles,state)
1393set(handles.i_txt,'Visible',state)
1394set(handles.num_first_i,'Visible',state)
1395set(handles.num_last_i,'Visible',state)
1396set(handles.num_incr_i,'Visible',state)
1397
1398%-----------------------------------
1399function enable_j(handles,state)
1400set(handles.j_txt,'Visible',state)
1401set(handles.num_first_j,'Visible',state)
1402set(handles.num_last_j,'Visible',state)
1403set(handles.num_incr_j,'Visible',state)
1404set(handles.MinIndex_j,'Visible',state)
1405set(handles.MaxIndex_j,'Visible',state)
1406
1407
1408%%%%%%%%%%%%%%%%%%%%
1409%%  MAIN ActionName FUNCTIONS
1410%%%%%%%%%%%%%%%%%%%%
1411%------------------------------------------------------------------------
1412% --- Executes on button press in RUN.
1413%------------------------------------------------------------------------
1414function RUN_Callback(hObject, eventdata, handles)
1415
1416%% settings of the button RUN
1417if ~isequal(get(handles.ActionInput,'BackgroundColor'),[1 0 0])
1418    msgbox_uvmat('ERROR','first activate the button ActionInput')
1419    return
1420end
1421set(handles.RUN,'BusyAction','queue'); % activation of STOP button will set BusyAction to 'cancel'
1422set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1423set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1424drawnow
1425set(handles.status,'Value',0)% desable status display if relevant
1426status_Callback([], eventdata, handles)
1427
1428%% launch action
1429errormsg=launch_action(handles);
1430if ~isempty(errormsg)
1431     msgbox_uvmat('ERROR',errormsg)
1432end
1433
1434%% reset the GUI series
1435update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1436set(handles.RUN, 'Enable','On')
1437set(handles.RUN,'BackgroundColor',[1 0 0])
1438set(handles.RUN, 'Value',0)
1439
1440%------------------------------------------------------------------------
1441% --- called by RUN_Callback
1442%------------------------------------------------------------------------
1443% The calculations are launched in three different ways:
1444% RunMode='local': calculation on the local Matlab session, will prevent other actions during that time.
1445% RunMode='background': calculation on the local computer, but in a new Matlab session (with no graphic output).
1446% RunMode='cluster': calculations dispatched in a cluster, using a managing system, 'oar, 'sge, or 'sgb'.
1447% In the latter case, the calculation is split in 'packets' of i index (all j indices are contained in a single packet).
1448% This splitting is possible only if the different calculations in the series are independent. Otherwise the action
1449% function imposes a number of processes NbSlice in input, for instance NbSlice=1 for a time series.
1450% If NbSlice is not imposed, the splitting in packets (jobs) is determined
1451% so that a job is optimum length AdvisedJobCPUTime), and the total job number in any case smaller
1452% than MaxJobNumber (these parameters are defined in the file series.xml in
1453% accordance with the management strategy for the cluster). The jobs are
1454% dispatched in parallel into NbCore processors by the cluster managing system.
1455
1456function errormsg=launch_action(handles)
1457errormsg=''; % default
1458
1459%% read the data on the GUI series
1460Param=read_GUI_series(handles); % displayed parameters
1461SeriesData=get(handles.series,'UserData'); % hidden parameters
1462if isfield(SeriesData,'TransformInput')
1463    Param.TransformInput=SeriesData.TransformInput;
1464end
1465if isfield(SeriesData,'ProjObject')
1466    Param.ProjObject=SeriesData.ProjObject;
1467end
1468if ~isfield(SeriesData,'i1_series')
1469    errormsg='The input field series needs to be refreshed: press REFRESH';
1470    return
1471end
1472if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'add_field...')
1473    errormsg='input field name(s) not defined, select add_field...';
1474    return
1475end
1476
1477%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1478RunMode='local'; % default (needed for first opening of the GUI series)
1479if isfield(Param.Action,'RunMode')
1480    RunMode=Param.Action.RunMode;
1481    Param.Action=rmfield(Param.Action,'RunMode'); % remove from the recorded xml file to avoid interference during ImportConfig
1482    Param.RunMode=RunMode; % keep track of the mode
1483end
1484ActionExt='.m'; % default
1485if isfield(Param.Action,'ActionExt')
1486    ActionExt=Param.Action.ActionExt; % '.m', '.sh' (compiled)  or '.py' (Python)
1487    Param.Action=rmfield(Param.Action,'ActionExt'); % remove from the recorded xml file to avoid interference during ImportConfig
1488end
1489ActionName=Param.Action.ActionName;
1490ActionPath=Param.Action.ActionPath;
1491path_series=fileparts(which('series'));
1492
1493%% create the Action fct handle if RunMode option = 'local'
1494if strcmp(RunMode,'local')
1495    if ~isequal(ActionPath,path_series)
1496        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1497        if ~exist(ActionPath,'dir')
1498            errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1499            return
1500        end
1501        if ~isequal(spath,ActionPath)
1502            addpath(ActionPath)% add the prescribed path if not the current one
1503        end
1504    end
1505    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1506    if ~isequal(ActionPath,path_series)
1507        rmpath(ActionPath)% add the prescribed path if not the current one
1508    end
1509end
1510
1511%% Get  parameters from series.xml
1512errormsg=''; % default error message
1513ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);
1514
1515%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled
1516if strcmp(ActionExt,'.sh')
1517    TransformPath='';
1518    if isfield(SeriesData,'TransformPath')
1519        TransformPath=SeriesData.TransformPath;
1520        if isfield(SeriesData,'TransformList')
1521            TransformList=get(handles.TransformName,'String');
1522            TransformIndex=get(handles.TransformName,'Value');
1523            TransformName=TransformList{TransformIndex};
1524            if ~ismember(TransformName,SeriesData.TransformList)
1525                TransformPath='';
1526            end
1527        end
1528    end
1529    if ~isempty(TransformPath)&&...
1530          ~strcmp(TransformPath,get(handles.TransformPath,'String'))% if the transform is not in paths set for compilation
1531        msgbox_uvmat('ERROR', 'compilation not available for this transform function, select .m')
1532        return
1533    end
1534    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1535    set(handles.ActionExt,'BackgroundColor',[1 1 0])
1536    [mcrmajor, mcrminor] = mcrversion;   
1537    MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
1538    RunTime = getenv('MCRROOT'); % Just variable MCRROOT with no version in it's name
1539    if strcmp(RunTime,'')
1540        RunTime = getenv(MCRROOT); % Use specialize MCRROOT with version
1541    end
1542    ActionNameVersion=[ActionName '_' MCRROOT];
1543    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
1544    % compile the .m file if the .sh file does not exist yet
1545    if ~exist(ActionFullName,'file')
1546        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1547        if strcmp(answer,'Yes')
1548            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1549            path_uvmat=fileparts(which('series'));
1550            currentdir=pwd;
1551            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1552            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1553            compile(ActionName,TransformPath)
1554            cd(currentdir)
1555        else
1556            errormsg='Action launch interrupted';
1557            return
1558        end       
1559    else
1560        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
1561        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1562        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1563            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1564            drawnow
1565            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
1566            if strcmp(answer,'Yes')
1567                path_uvmat=fileparts(which('series'));
1568                currentdir=pwd;
1569                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1570                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1571                addpath(fullfile(path_uvmat,'transform_field'))% add the path to transform functions to run the fct 'compile'
1572                compile(ActionName,TransformPath)
1573                cd(currentdir)
1574            end
1575        end
1576    end
1577
1578    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1579     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1580end
1581
1582%% set nbre of cluster cores and processes:
1583% NbCore is the number of computer processors used
1584% NbProcess is the number of independent processes in which the required calculation is split.
1585switch RunMode
1586    case {'local','background'}
1587        NbCore=1; % no need to split the calculation
1588    case 'cluster'
1589        %proposed number of cores to reserve in the cluster
1590        NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised;
1591        NbCoreMax=SeriesData.SeriesParam.ClusterParam.NbCoreMax;
1592        if NbCoreMax~=1
1593            if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1594                warning_string=', preferably use .sh option to save Matlab licences';
1595            else
1596                warning_string=')';
1597            end
1598            answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised));
1599            if isempty(answer)
1600                errormsg='Action launch interrupted by user';
1601                return
1602            end
1603            NbCore=str2double(answer);
1604            if NbCore > NbCoreMax
1605                NbCore=NbCoreMax;
1606            end
1607        else
1608            NbCore=1;
1609        end
1610end
1611if ~isfield(Param.IndexRange,'NbSlice')
1612    Param.IndexRange.NbSlice=[];
1613end
1614OutputPath=get(handles.OutputPath,'String');
1615
1616%% Look for processing on multiple experiments set by the GUI browse_data
1617NbExp=1;% initiate the number of experiments set by the GUI browse_data, =1 otherwise
1618if get(handles.Replicate,'Value')
1619    hh=findobj(allchild(0),'Tag','browse_data');
1620    if isempty(hh)
1621        set(handles.Replicate,'Value',0)
1622    else
1623        set(handles.Replicate,'BackgroundColor',[1 1 0])%paint Relicate button in yellow
1624        BrowseData=guidata(hh);
1625        SourceDir=get(BrowseData.SourceDir,'String');
1626        ListExp=get(BrowseData.ListExperiments,'String');
1627        ExpIndices=get(BrowseData.ListExperiments,'Value');
1628        ListExp=ListExp(ExpIndices);
1629        ListDevices=get(BrowseData.ListDevices,'String');
1630        DeviceIndices=get(BrowseData.ListDevices,'Value');
1631        ListDevices=ListDevices(DeviceIndices);
1632        ListDataSeries=get(BrowseData.DataSeries,'String');
1633        DataSeriesIndices=get(BrowseData.DataSeries,'Value');
1634        ListDataSeries=ListDataSeries(DataSeriesIndices);
1635        NbExp=0; % counter of the number of experiments set by the GUI browse_data
1636        for iexp=1:numel(ListExp)
1637            if ~isempty(regexp(ListExp{iexp},'^\+/'))% if it is a folder
1638               %if strcmp(get(BrowseData.DataSeries,'enable'),'off') %case of a multiple input line for series
1639%                     NbExp=NbExp+1;
1640%                     ExpIndex{NbExp}=iexp;
1641%                     for idevice=1:numel(ListDevices)
1642%                         lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
1643%                             regexprep(ListDevices{idevice},'^\+/',''));
1644%                         lpathout=fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),...
1645%                             regexprep(ListDevices{idevice},'^\+/',''));
1646%                         ldir=regexprep(ListDataSeries{idevice},'^\+/','');
1647%                         ListPath{idevice,NbExp}=lpath;
1648%                         ListPathOut{idevice,NbExp}=lpathout;
1649%                         ListSubdir{idevice,NbExp}=ldir;
1650%                     end
1651                %else
1652                    for idevice=1:numel(ListDevices)
1653                        if ~isempty(regexp(ListDevices{idevice},'^\+/'))% if it is a folder
1654                            for isubdir=1:numel(ListDataSeries)
1655                                if ~isempty(regexp(ListDataSeries{isubdir},'^\+/'))% if it is a folder
1656                                    lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
1657                                        regexprep(ListDevices{idevice},'^\+/',''));
1658                                    lpathout= fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),...
1659                                        regexprep(ListDevices{idevice},'^\+/',''));
1660                                    ldir= regexprep(ListDataSeries{isubdir},'^\+/','');
1661                                    if exist(fullfile(lpath,ldir),'dir')
1662                                        NbExp=NbExp+1;
1663                                        ExpIndex(NbExp)=ExpIndices(iexp);
1664                                        DeviceIndex(NbExp)=DeviceIndices(idevice);
1665                                        ListPath{NbExp}=lpath;
1666                                        ListPathOut{NbExp}=lpathout;
1667                                        ListDeviceOut{NbExp}=regexprep(ListDevices{idevice},'^\+/','');
1668                                        ListExpOut{NbExp}=regexprep(ListExp{iexp},'^\+/','');
1669                                        ListSubdir{NbExp}=ldir;
1670                                    end
1671                                end
1672                            end
1673                        end
1674                    end
1675%                 end
1676            end
1677        end
1678        answer=msgbox_uvmat('INPUT_Y-N-Cancel',['replicate the processing on ' num2str(NbExp) ' data series']);
1679        if strcmp(answer,'Cancel')||strcmp(answer,'No')
1680            return
1681        end
1682    end
1683end
1684
1685%%%%%%%%%%%%%%%%%%% LOOP ON EXPERIMENTS POSSIBLY SET BY THE GUI browse_data, NbExp=1 otherwise %%%%%%%%%
1686
1687for iexp=1:NbExp
1688    if get(handles.Replicate,'Value')
1689        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1690            disp('program stopped by user')
1691            return
1692        end
1693        set(BrowseData.ListExperiments,'Value',ExpIndex(iexp))
1694        set(BrowseData.ListDevices,'Value',DeviceIndex(iexp))
1695        Param.InputTable(:,1)=ListPath(:,iexp);
1696        Param.InputTable(:,2)=ListSubdir(:,iexp);
1697        OutputSubDir=unique(ListSubdir(:,iexp));
1698        Param.OutputSubDir=OutputSubDir{1};
1699        if numel(OutputSubDir)>1% case
1700            for iout=2:numel(OutputSubDir)
1701                Param.OutputSubDir=[Param.OutputSubDir '-' OutputSubDir{iout}];
1702            end               
1703        end       
1704    end
1705    [xx,ExpName]=fileparts(Param.InputTable{1,1});
1706    Param.IndexRange.first_i=str2num(get(handles.num_first_i,'String'));%reset the firrst_i and last_i for multiple experiments, modified by the splitting into NbProcess
1707    Param.IndexRange.last_i=str2num(get(handles.num_last_i,'String'));
1708   
1709    %% create the output data directory if needed, after checking its existence
1710    OutputDir='';
1711    answer='';
1712    if isfield(Param,'OutputSubDir')&& isfield(Param,'OutputDirExt')% possibly update the output dir if it already exists
1713        PathOut=get(handles.OutputPath,'String');
1714        if ~exist(PathOut,'dir') % test if  the dir  already exist
1715            PathOut=uigetdir(PathOut,'pick the output root path');
1716            set(handles.OutputPath,'String',PathOut);
1717        end
1718        if get(handles.Replicate,'Value')
1719        PathExpOut=fileparts(ListPath{iexp});
1720        PathExpDeviceOut=ListPath{iexp};
1721        else
1722            PathExpOut=fullfile(PathOut,get(handles.Experiment,'String'));
1723            PathExpDeviceOut=fullfile(PathExpOut,get(handles.Device,'String'))
1724        end
1725        if ~exist(PathExpOut,'dir')
1726            [tild,msg1]=mkdir(PathExpOut);
1727            if ~strcmp(msg1,'')
1728                errormsg=['cannot create ' PathExpOut ': ' msg1]; % error message for directory creation
1729                return
1730            end
1731        end
1732        if ~exist(PathExpDeviceOut,'dir')
1733            [tild,msg1]=mkdir(PathExpDeviceOut);
1734            if ~strcmp(msg1,'')
1735                errormsg=['cannot create ' PathExpDeviceOut ': ' msg1]; % error message for directory creation
1736                return
1737            end
1738        end
1739
1740        SubDirOut=[Param.OutputSubDir Param.OutputDirExt];
1741        SubDirOutNew=SubDirOut;
1742        detect=exist(fullfile(PathExpDeviceOut,SubDirOutNew),'dir'); % test if  the dir  already exist
1743        check_create=1; % need to create the result directory by default
1744        CheckOverwrite=1;
1745        if isfield(Param,'CheckOverwrite')
1746            CheckOverwrite=Param.CheckOverwrite;% will overwrite previous data if it is equal to 1
1747        end
1748        while detect
1749            if CheckOverwrite
1750                comment=', possibly overwrite previous data';
1751            else
1752                comment=', will complement existing result files (no overwriting)';
1753            end
1754            answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(PathExpDeviceOut,SubDirOutNew) comment]);
1755            if strcmp(answer,'Cancel')
1756                break
1757            elseif strcmp(answer,'Yes')
1758                detect=0;
1759                check_create=0;
1760            else
1761                r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names'); % detect whether name ends by a number
1762                if isempty(r)
1763                    r(1).root=[SubDirOutNew '_'];
1764                    r(1).num1='0';
1765                end
1766                SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1
1767                detect=exist(fullfile(PathExpDeviceOut,SubDirOutNew),'dir'); % test if  the dir  already exists
1768                check_create=1;
1769            end
1770        end
1771        if strcmp(answer,'Cancel')
1772            continue
1773        end
1774        Param.OutputDirExt=regexprep(SubDirOutNew,['^' Param.OutputSubDir],'');
1775        Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output
1776        OutputDir=fullfile(PathExpDeviceOut,[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
1777        if check_create    % create output directory if it does not exist
1778            [tild,msg1]=mkdir(OutputDir);
1779            if ~strcmp(msg1,'')
1780                errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
1781                return
1782            end
1783        end
1784       
1785    elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1786        OutputDir=Param.ActionInput.LogPath;
1787    end
1788    if isfield(Param,'OutputSubDir')&& isfield(Param,'OutputDirExt')
1789        set(handles.OutputSubDir,'String',Param.OutputSubDir)
1790        set(handles.OutputDirExt,'String',Param.OutputDirExt)
1791        drawnow
1792    end
1793    if get(handles.Replicate,'Value')
1794        set(handles.InputTable,'Data',Param.InputTable)
1795        set(handles.OutputPath,'String',OutputPath)
1796         set(handles.Experiment,'String',ListExpOut{iexp})
1797        set(handles.Device,'String',ListDeviceOut{iexp})
1798        Param.Experiment=ListExpOut{iexp};
1799        Param.Device=ListDeviceOut{iexp};
1800        check_input_file_series(handles)     
1801    end
1802    DirXml=fullfile(OutputDir,'0_XML');
1803    if ~exist(DirXml,'dir')
1804        [~,msg1]=mkdir(DirXml);
1805        if ~strcmp(msg1,'')
1806            errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation
1807            return
1808        end
1809        [success,msg] = fileattrib(DirXml,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1810        if success==0
1811            msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg}); % error message for directory creation
1812        end
1813    end
1814    OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files
1815   
1816    %% get the set of reference input field indices
1817    first_i=1; % first i index to process
1818    last_i=1; % last i index to process
1819    incr_i=1; % increment step in i index
1820    first_j=1; % first j index to process
1821    last_j=1; % last j index to process
1822    incr_j=1; % increment step in j index
1823    if isfield(Param.IndexRange,'first_i')
1824        first_i=Param.IndexRange.first_i;
1825        incr_i=Param.IndexRange.incr_i;
1826        last_i=Param.IndexRange.last_i;
1827    end
1828    if isfield(Param.IndexRange,'incr_j')
1829        first_j=Param.IndexRange.first_j;
1830        last_j=Param.IndexRange.last_j;
1831        incr_j=Param.IndexRange.incr_j;
1832    end
1833    if last_i < first_i || last_j < first_j
1834        errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
1835        return
1836    end
1837    %incr_i must be defined, =1 by default, if NbSlice is active
1838    if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1839        incr_i=1;
1840        set(handles.num_incr_i,'String','1')
1841    end
1842    % case of no increment i defined: processing is done on the available files found in i1_series
1843    if isempty(incr_i)
1844        if isempty(incr_j)
1845            [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1846            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1847            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1848            ref_j=ref_j-1;
1849            ref_i=ref_i-1;
1850        else
1851            ref_j=first_j:incr_j:last_j;
1852            [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1853            ref_i=ref_i-1;
1854            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1855        end
1856        % increment i is defined: processing is done on first_i:incr_i:last_i;
1857    else
1858        ref_i=first_i:incr_i:last_i;
1859        if isempty(incr_j)% automatic finding of the existing j indices
1860            [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1861            ref_j=ref_j-1;
1862            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1863        else
1864            ref_j=first_j:incr_j:last_j;
1865        end
1866    end
1867    nbfield_j=numel(ref_j); % number of j indices
1868    BlockLength=numel(ref_i); % by default, job involves the full set of i field indices
1869    NbProcess=1;
1870    switch RunMode
1871        case 'cluster'
1872            if (isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime))
1873                CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
1874            else
1875                answer=msgbox_uvmat('INPUT_TXT','estimate the CPU time(in minutes) for each value of index i:' ,'');
1876                CPUTime=str2num(answer);
1877                set(handles.num_CPUTime,'String',answer)
1878                Param.Action.CPUTime=CPUTime;
1879            end
1880            JobNumberMax=SeriesData.SeriesParam.ClusterParam.JobNumberMax;
1881            JobCPUTimeAdvised=SeriesData.SeriesParam.ClusterParam.JobCPUTimeAdvised;
1882            if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
1883                BlockLength= ceil(JobCPUTimeAdvised/(CPUTime*nbfield_j)); % iterations are grouped in sets with length BlockLength  such that the typical CPU time of a job is JobCPUTimeAdvised.
1884                BlockLength=max(BlockLength,ceil(numel(ref_i)*NbExp/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs
1885                NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
1886            else
1887                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1888            end
1889            NbCore=min(NbCore,NbProcess); % reduces the number of cores if it exceeds the number of processes
1890        otherwise
1891            if ~isempty(Param.IndexRange.NbSlice)
1892                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1893            end
1894    end
1895   
1896    %% record nbre of output files and starting time for computation for status
1897    StatusData=get(handles.status,'UserData');
1898    if isfield(StatusData,'OutputFileMode')
1899        switch StatusData.OutputFileMode
1900            case 'NbInput'
1901                StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1902            case 'NbInput_i'
1903                StatusData.NbOutputFile=numel(ref_i);
1904            case 'NbSlice'
1905                StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1906        end
1907    end
1908    StatusData.TimeStart=now;
1909    set(handles.status,'UserData',StatusData)
1910   
1911    %% case of a function in Python
1912    if strcmp(ActionExt, '.py (in dev.)')
1913        fprintf([
1914            '\n' ...
1915            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1916            'The option .py is used. It is still in development.\n' ...
1917            'To try it, first install pyper and the most recent version of fluidimage\n' ...
1918            '(see https://bitbucket.org/fluiddyn/fluidimage).\n' ...
1919            'Warning: there is no direct correspondance between UVMAT and fluidimage parameters\n' ...
1920            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1921        RunMode = 'python';
1922    end
1923   
1924   
1925    %% direct processing on the current Matlab session or creation of command files
1926    filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters
1927    extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
1928    for iprocess=1:NbProcess
1929        extxml{iprocess}='.xml';
1930    end
1931    for iprocess=1:NbProcess
1932        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1933            disp('program stopped by user')
1934            return
1935        end
1936        Param.IndexRange.incr_slice=incr_i;
1937        if isempty(Param.IndexRange.NbSlice)
1938            Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1939            if Param.IndexRange.first_i>last_i
1940                NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation
1941                break
1942            end
1943            Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1944        else %multislices (then incr_i is not empty)
1945            Param.IndexRange.first_i= first_i+iprocess-1;
1946            Param.IndexRange.incr_slice=incr_i*Param.IndexRange.NbSlice;
1947        end
1948        for ilist=1:size(Param.InputTable,1)
1949            Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
1950        end
1951       
1952        if isfield(Param,'OutputSubDir')
1953            t=struct2xml(Param);
1954            t=set(t,1,'name','Series');
1955            extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
1956                Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1957            filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
1958            try
1959                save(t, filexml{iprocess}); % save the xml file containing the processing parameters
1960            catch ME
1961                if ~strcmp (RunMode,'local')
1962                    errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
1963                    return
1964                end
1965            end
1966        end
1967        if strcmp (RunMode,'local')
1968            switch ActionExt
1969                case '.m'
1970                    h_fun(Param); % direct launching
1971                   
1972                case '.sh'
1973                    switch computer
1974                        case {'PCWIN','PCWIN64'} %Windows system
1975                            filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters
1976                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system
1977                        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1978                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);
1979                    end
1980            end
1981        end
1982    end
1983   
1984    if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
1985        %% processing on a different session of the same computer (background) or cluster, create executable files
1986        batch_file_list=cell(NbProcess,1); % initiate the list of executable files
1987        DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files
1988        switch computer
1989            case {'PCWIN','PCWIN64'} %Windows system
1990                ExeExt='.bat';
1991            case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1992                ExeExt='.sh';
1993        end
1994        %create subdirectory for executable files
1995        if ~exist(DirExe,'dir')
1996            [tild,msg1]=mkdir(DirExe);
1997            if ~strcmp(msg1,'')
1998                errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation
1999                return
2000            end
2001            [success,msg] = fileattrib(DirExe,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2002            if success==0
2003                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirExe ':']; msg}); % error message for directory creation
2004            end
2005        end
2006        %create subdirectory for log files
2007        DirLog=fullfile(OutputDir,'0_LOG');
2008        if ~exist(DirLog,'dir')
2009            [tild,msg1]=mkdir(DirLog);
2010            if ~strcmp(msg1,'')
2011                errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation
2012                return
2013            end
2014            [success,msg] = fileattrib(DirLog,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2015            if success==0
2016                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirLog ':']; msg}); % error message for directory creation
2017            end
2018        end
2019       
2020        %create the executable file
2021        file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
2022            first_i,last_i,first_j,last_j);
2023        file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
2024        filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
2025            first_i,last_i,first_j,last_j);
2026        filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
2027       
2028        for iprocess=1:NbProcess
2029            %create the executable file
2030            batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt));
2031           
2032            % set the log file name
2033            filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));
2034        end
2035    end
2036   
2037    %% launch the executable files for background or cluster processing
2038   
2039    switch RunMode
2040       
2041        case 'background'
2042            [fid,message]=fopen(file_exe_global,'w');
2043            if isequal(fid,-1)
2044                errormsg=['creation of ' file_exe_global ':' message];
2045                return
2046            end
2047            switch ActionExt
2048                case '.m'% Matlab function
2049                    switch computer
2050                        case {'GLNX86','GLNXA64','MACI64'}
2051                            matlab_ver = ver('MATLAB');
2052                            matlab_version = matlab_ver.Version;
2053                            cmd=[...
2054                                '#!/bin/bash\n'...
2055                                'source /etc/profile\n'...
2056                                'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
2057                                'time_start=$(date +%%s)\n'...
2058                                'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <<END_MATLAB\n'...
2059                                'addpath(''' path_series ''');\n'...
2060                                'addpath(''' Param.Action.ActionPath ''');\n'];
2061                            for iprocess=1:NbProcess
2062                                cmd=[cmd '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'];
2063                            end
2064                            cmd=[cmd  'exit\n' 'END_MATLAB\n'...
2065                                'time_end=$(date +%%s)\n'...
2066                                'echo "global time = " $(($time_end - $time_start)) >> ''' filelog_global '''\n'];
2067                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2068                            fclose(fid); % close the executable filefilelog_global
2069                            system(['chmod +x ' file_exe_global]); % set the file to executable
2070                        case {'PCWIN','PCWIN64'}
2071                            cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
2072                                ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
2073                                'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
2074                            for iprocess=1:NbProcess
2075                                cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
2076                            end
2077                            cmd=[cmd ';exit"'];
2078                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2079                            fclose(fid); % close the executable file
2080                    end
2081                    system([file_exe_global ' &'])% directly execute the command file
2082                case '.sh' % compiled Matlab function
2083                    for iprocess=1:NbProcess
2084                        switch computer
2085                            case {'GLNX86','GLNXA64','MACI64'}
2086                                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2087                                if isequal(fid,-1)
2088                                    errormsg=['creation of .bat file: ' message];
2089                                    return
2090                                end
2091                                cmd=['#!/bin/bash \n '...
2092                                    '#$ -cwd \n '...
2093                                    'hostname && date \n '...
2094                                    'umask 002 \n'...
2095                                    ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2096                                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2097                                fclose(fid); % close the executable file
2098                                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2099                                system([batch_file_list{iprocess} ' &'])% directly execute the command file
2100                            case {'PCWIN','PCWIN64'}
2101                                msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
2102                                return
2103                        end
2104                    end
2105                    msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background for ' ExpName ': press STATUS to see results'])
2106            end
2107           
2108        case 'cluster' % option 'oar-parexec' used
2109            %create subdirectory for oar commands
2110            for iprocess=1:NbProcess
2111                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2112                if isequal(fid,-1)
2113                    errormsg=['creation of .bat file: ' message];
2114                    return
2115                end
2116                if  strcmp(ActionExt,'.sh')
2117                    cmd=['#!/bin/bash \n '...
2118                        '#$ -cwd \n '...
2119                        'hostname && date \n '...
2120                        'umask 002 \n'...
2121                        ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2122                else
2123                    matlab_ver = ver('MATLAB');
2124                    matlab_version = matlab_ver.Version;
2125                    cmd=[...
2126                        '#!/bin/bash\n'...
2127                        'source /etc/profile\n'...
2128                        'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
2129                        'matlab -nodisplay -nosplash -nojvm -singleCompThread -logfile ''' filelog{iprocess} ''' <<END_MATLAB\n'...
2130                        'addpath(''' path_series ''');\n'...
2131                        'addpath(''' Param.Action.ActionPath ''');\n'...
2132                        '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'...
2133                        'exit\n'...
2134                        'END_MATLAB\n'];
2135                end
2136                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2137                fclose(fid); % close the executable file
2138                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2139            end
2140            DIR_CLUSTER=fullfile(OutputDir,'0_CLUSTER');
2141            if exist(DIR_CLUSTER,'dir')% delete the content of the dir 0_LOG to allow new input
2142                curdir=pwd;
2143                cd(DIR_CLUSTER)
2144                delete('*')
2145                cd(curdir)
2146            else
2147                [tild,msg1]=mkdir(DIR_CLUSTER);
2148                if ~strcmp(msg1,'')
2149                    errormsg=['cannot create ' DIR_CLUSTER ': ' msg1]; % error message for directory creation
2150                    return
2151                end
2152            end
2153            % create file containing the list of jobs
2154            ListProcess=fullfile(DIR_CLUSTER,'job_list.txt'); % name of the file containing the list of executables
2155            [fid,errormsg]=fopen(ListProcess,'w'); % open it for writting
2156            if isempty(errormsg)
2157            for iprocess=1:length(batch_file_list)
2158                fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files
2159            end
2160            fclose(fid);
2161            system(['chmod +x ' ListProcess]); % set the file to executable
2162            else
2163                errormsg=['error for writting the executable file:' errormsg];
2164            end       
2165            CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes)
2166            LaunchCmdFcn=SeriesData.SeriesParam.ClusterParam.LaunchCmdFcn;
2167            oar_command=feval(LaunchCmdFcn,ListProcess,ActionFullName,DirLog,NbProcess, NbCore,CPUTimeProcess)
2168            [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
2169            filename_oarcommand=fullfile(DIR_CLUSTER,'0_cluster_command'); % keep track of the command in file '0-OAR/0_cluster_command'
2170            [fid,errormsg]=fopen(filename_oarcommand,'w');
2171            if ~isempty(errormsg)
2172                msgbox_uvmat('ERROR',['cannot create ' filename_oarcommand ': ' errormsg])
2173                return
2174            end
2175            fprintf(fid,oar_command); % store the command
2176            fprintf(fid,result); % store the result (job ID number)
2177            fclose(fid);
2178            if status==0
2179                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched for ' ExpName ' as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
2180            else
2181                msgbox_uvmat('ERROR',result)
2182            end
2183            %     case 'cluster_pbs' % for LMFA Kepler machine:  trqnsferred to fct
2184           
2185            %         %create subdirectory for pbs command and log files
2186            %         DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS
2187            %         if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
2188            %             curdir=pwd;
2189            %             cd(DirPBS)
2190            %             delete('*')
2191            %             cd(curdir)
2192            %         else
2193            %             [tild,msg1]=mkdir(DirPBS);
2194            %             if ~strcmp(msg1,'')
2195            %                 errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation
2196            %                 return
2197            %             end
2198            %         end
2199            %         max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
2200            %         walltime_onejob=1800; % seconds, max estimated time for asingle file index value
2201            %         ListProcess=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file
2202            %         fid=fopen(ListProcess,'w');
2203            %         for iprocess=1:length(batch_file_list)
2204            %             fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files
2205            %         end
2206            %         fclose(fid);
2207            %         system(['chmod +x ' ListProcess]); % set the file to executable
2208            %         pbs_command=['qsub -n CIVX '...
2209            %             '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
2210            %             '-l /core=' num2str(NbCore) ','...
2211            %             'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
2212            %             '-E ' regexprep(ListProcess,'\.txt\>','.stderr') ' '...
2213            %             '-O ' regexprep(ListProcess,'\.txt\>','.log') ' '...
2214            %             extra_qstat ' '...
2215            %             '"oar-parexec -s -f ' ListProcess ' '...
2216            %             '-l ' ListProcess '.log"'];
2217            %         filename_oarcommand=fullfile(DirPBS,'pbs_command');
2218            %         fid=fopen(filename_oarcommand,'w');
2219            %         fprintf(fid,pbs_command);
2220            %         fclose(fid);
2221            %         fprintf(pbs_command); % display in command line
2222            %         %system(pbs_command);
2223            %         msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
2224           
2225        case 'cluster_sge' % for PSMN % TODO: use the standard 'cluster' config with an external fct
2226            % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs
2227            % o?? N < 1000.
2228            %create subdirectory for pbs command and log files
2229           
2230            DirSGE=fullfile(OutputDir,'0_SGE');
2231            if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input
2232                curdir=pwd;
2233                cd(DirSGE)
2234                delete('*')
2235                cd(curdir)
2236            else
2237                [tild,msg1]=mkdir(DirSGE);
2238                if ~strcmp(msg1,'')
2239                    errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
2240                    return
2241                end
2242            end
2243            maxImgsPerJob = ceil(length(batch_file_list)/NbCore);
2244            disp(['Max number of jobs: ' num2str(NbCore)])
2245            disp(['Images per job: ' num2str(maxImgsPerJob)])
2246           
2247            iprocess = 1;
2248            imgsInJob = [];
2249            currJobIndex = 1;
2250            done = 0;
2251            while(~done)
2252                if(iprocess <= length(batch_file_list))
2253                    imgsInJob = [imgsInJob, iprocess];
2254                end
2255                if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list)))
2256                    cmd=['#!/bin/sh \n'...
2257                        '#$ -cwd \n'...
2258                        'hostname && date\n']
2259                    for ii=1:numel(imgsInJob)
2260                        cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
2261                    end
2262                    [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
2263                    fprintf(fid, cmd);
2264                    fclose(fid);
2265                    system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh'])
2266                    sge_command=['qsub -N civ_' num2str(currJobIndex) ' '...
2267                        '-q ' qstat_Queue ' '...
2268                        '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2269                        '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2270                        fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
2271                    fprintf(sge_command); % display in command line
2272                    [status, result] = system(sge_command);
2273                    fprintf(result);
2274                    currJobIndex = currJobIndex + 1;
2275                    imgsInJob = [];
2276                end
2277                if(iprocess == length(batch_file_list))
2278                    done = 1;
2279                end
2280                iprocess = iprocess + 1;
2281            end
2282            msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.'])
2283        case 'python'
2284            command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ...
2285                'python -m fluidimage.run_from_xml ' filexml{iprocess}];
2286            fprintf(['command:\n' command '\n\n'])
2287            system(command, '-echo');
2288    end
2289    if exist(OutputDir,'dir')
2290        [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir);
2291        if MESSAGE.GroupWrite~=1
2292            [success,msg] = fileattrib(OutputDir,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2293            if success==0
2294                msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg}); % error message for directory creation
2295            end
2296        end
2297    end
2298end
2299set(handles.Replicate,'BackgroundColor',[0 1 0])
2300
2301%------------------------------------------------------------------------
2302function STOP_Callback(hObject, eventdata, handles)
2303%------------------------------------------------------------------------
2304set(handles.RUN, 'BusyAction','cancel')
2305set(handles.RUN,'BackgroundColor',[1 0 0])
2306set(handles.RUN,'enable','on')
2307set(handles.RUN, 'Value',0)
2308
2309%------------------------------------------------------------------------
2310% --- read parameters from the GUI series
2311%------------------------------------------------------------------------
2312function Param=read_GUI_series(handles)
2313
2314%% read raw parameters from the GUI series
2315Param=read_GUI(handles.series);
2316
2317%% clean the output structure by removing unused information
2318if isfield(Param,'Pairs')
2319    Param=rmfield(Param,'Pairs'); % info Pairs not needed for output
2320end
2321if isfield(Param,'InputLine')
2322    Param=rmfield(Param,'InputLine');
2323end
2324if isfield(Param,'EditObject')
2325    Param=rmfield(Param,'EditObject');
2326end
2327Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2328Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2329empty_line=false(size(Param.InputTable,1),1);
2330for iline=1:size(Param.InputTable,1)
2331    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2332end
2333Param.InputTable(empty_line,:)=[];
2334
2335%------------------------------------------------------------------------
2336% --- Executes on selection change in ActionName.
2337function ActionName_Callback(hObject, ActionPath, handles)
2338%------------------------------------------------------------------------
2339
2340%% stop any ongoing series processing
2341if isequal(get(handles.RUN,'Value'),1)
2342    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2343    if strcmp(answer,'Yes')
2344        STOP_Callback(hObject, [], handles)
2345    else
2346        return
2347    end
2348end
2349set(handles.ActionName,'BackgroundColor',[1 1 0])
2350huigetfile=findobj(allchild(0),'tag','status_display');
2351if ~isempty(huigetfile)
2352    delete(huigetfile)
2353end
2354drawnow
2355
2356%% get Action name and path
2357NbBuiltinAction=get(handles.Action,'UserData'); % nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2358ActionList=get(handles.ActionName,'String'); % list menu fields
2359ActionIndex=get(handles.ActionName,'Value');
2360if ~isequal(ActionIndex,1)% if we are not just opening series
2361    InputTable=get(handles.InputTable,'Data');
2362    if isempty(InputTable{1,4})
2363        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2364        return
2365    end
2366end
2367ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2368ActionPathList=get(handles.ActionName,'UserData'); % list of recorded paths to functions of the list ActionName
2369
2370%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2371if isequal(ActionName,'more...')
2372    if ~ischar(ActionPath)
2373        ActionPath=get(handles.ActionPath,'String');
2374    end
2375    [FileName, PathName] = uigetfile( ...
2376        {'*.m', ' (*.m)';
2377        '*.m',  '.m files '; ...
2378        '*.*', 'All Files (*.*)'}, ...
2379        'Pick a series processing function ',ActionPath);
2380    if length(FileName)<2
2381        return
2382    end
2383    [tild,ActionName,ActionExt]=fileparts(FileName);
2384   
2385    % insert the choice in the menu ActionName
2386    ActionIndex=find(strcmp(ActionName,ActionList),1); % look for the selected function in the menu Action
2387    PathName=regexprep(PathName,'/$','');
2388    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2389        ActionIndex=[]; % the selected path is different than the recorded one
2390    end
2391    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2392        ActionIndex= length(ActionList);
2393        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)]; % the selected function is appended in the menu, before the last item 'more...'
2394         ActionPathList=[ActionPathList; PathName];
2395    end
2396   
2397    % record the file extension and extend the path list if it is a new extension
2398    ActionExtList=get(handles.ActionExt,'String');
2399    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2400    if isempty(ActionExtIndex)
2401        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2402    end
2403
2404    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
2405    if length(ActionList)>NbBuiltinAction+5; % nb_builtin_ACTION=nbre of functions always remaining in the initial menu
2406        nbremove=length(ActionList)-NbBuiltinAction-5;
2407        ActionList(NbBuiltinAction+1:end-5)=[];
2408        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2409        ActionIndex=ActionIndex-nbremove;
2410    end
2411   
2412    % record action menu, choice and path
2413    set(handles.ActionName,'Value',ActionIndex)
2414    set(handles.ActionName,'String',ActionList)
2415       set(handles.ActionName,'UserData',ActionPathList);
2416    set(handles.ActionExt,'Value',ActionExtIndex)
2417       
2418    %record the user defined menu additions in personal file profil_perso
2419    dir_perso=prefdir;
2420    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2421    if NbBuiltinAction+1<=numel(ActionList)-1
2422        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2423        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
2424        ActionExtListUser={};
2425        if numel(ActionExtList)>2
2426            ActionExtListUser=ActionExtList(3:end);
2427        end
2428        if exist(profil_perso,'file')
2429            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2430        else
2431            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2432        end
2433    end
2434end
2435
2436%% check the current ActionPath to the selected function
2437ActionPath=ActionPathList{ActionIndex}; % current recorded path
2438set(handles.ActionPath,'String',ActionPath); % show the path to the senlected function
2439
2440%% reinitialise the waitbar
2441update_waitbar(handles.Waitbar,0)
2442
2443%% Put the first line of the selected Action fct as tooltip help
2444try
2445    [fid,errormsg] =fopen([ActionName '.m']);
2446    InputText=textscan(fid,'%s',1,'delimiter','\n');
2447    fclose(fid);
2448    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2449end
2450set(handles.ActionName,'BackgroundColor',[1 1 1])
2451set(handles.ActionInput,'BackgroundColor',[1 0 1])% set ActionInput button to magenta color to indicate that input refr
2452set(handles.num_CPUTime,'String','')
2453
2454% --- Executes on button press in ActionInput.
2455function ActionInput_Callback(hObject, eventdata, handles)
2456
2457set(handles.ActionInput,'BackgroundColor',[1 1 0])
2458SeriesData=get(handles.series,'UserData'); % info on the input file series
2459
2460%% create the function handle for Action
2461ActionPath=get(handles.ActionPath,'String');
2462ActionList=get(handles.ActionName,'String');
2463ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2464if ~exist(ActionPath,'dir')
2465    ActionName_Callback(handles.ActionName, ActionPath, handles)% update the function
2466    return
2467end
2468current_dir=pwd; % current working dir
2469cd(ActionPath)
2470h_fun=str2func(ActionName);
2471cd(current_dir)
2472
2473%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
2474Param=read_GUI_series(handles); % read the parameters from the GUI series
2475Param.Action.RUN=0;
2476Param.SeriesData=SeriesData;
2477ParamOut=h_fun(Param); % run the selected Action function to get the relevant input
2478
2479
2480%% Visibility of VelType and VelType_1 menus asked by ActionName
2481VelTypeRequest=1; % VelType requested by default
2482VelTypeRequest_1=1; % VelType requested by default
2483if isfield(ParamOut,'VelType')
2484    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2485    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2486end
2487FieldNameRequest=0;  %hidden by default
2488FieldNameRequest_1=0;  %hidden by default
2489if isfield(ParamOut,'FieldName')
2490    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2491    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2492end
2493
2494%% Detect the types of input files and set menus and default options in 'VelType'
2495if ~isfield(SeriesData,'FileType')
2496    SeriesData.FileType={'none'};
2497end
2498iview_civ=find( strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
2499iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ
2500FieldList=get(handles.FieldName,'String'); % previous list as default
2501if ~iscell(FieldList),FieldList={FieldList};end
2502FieldList_1=get(handles.FieldName_1,'String'); % previous list as default
2503if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
2504CheckList_1=1; % indicate whether FieldName_1 has been updated
2505handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
2506if VelTypeRequest && numel(iview_civ)>=1
2507    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2508    set(handles.VelType,'Value',1)% set first choice by default
2509    set(handles.VelType,'String',[{'*'};menu])
2510    set(handles.VelType,'Visible','on')
2511    set(handles.VelType_title,'Visible','on')
2512    FieldList=set_field_list('U','V'); % standard menu for civx data
2513    if max(get(handles.FieldName,'Value'))>numel(FieldList)
2514        set(handles.FieldName,'Value',1); % velocity vector choice by default
2515    end
2516    if  VelTypeRequest_1 && numel(iview_civ)>=2
2517        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2518        set(handles.VelType_1,'Value',1)% set first choice by default
2519        set(handles.VelType_1,'String',[{'*'};menu])
2520        set(handles.VelType_1,'Visible','on')
2521        set(handles.VelType_title_1,'Visible','on')
2522        FieldList_1=[set_field_list('U','V');{'C'};{'add_field...'}]; % standard menu for civx data
2523        CheckList_1=1;
2524        set(handles.FieldName_1,'Value',1); % velocity vector choice by default
2525    else
2526        set(handles.VelType_1,'Visible','off')
2527        set(handles.VelType_title_1,'Visible','off')
2528    end
2529else
2530    set(handles.VelType,'Visible','off')
2531    set(handles.VelType_title,'Visible','off')
2532end
2533
2534%% Detect the types of input files and set menus and default options in 'FieldName'
2535if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
2536    set(handles.InputFields,'Visible','on')% set the frame InputFields visible
2537    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2538        set(handles.FieldName,'Visible','on')
2539        set(handles.Field_text,'Visible','on')
2540        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2541        ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2542        for ilist=1:numel(ind_var)
2543            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2544                FieldList={}; % previous choice not consistent with new input field
2545                set(handles.FieldName,'Value',1)
2546                break
2547            end
2548        end
2549        if ~isempty(FieldList)
2550            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2551                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2552                FieldList={};
2553                set(handles.Coord_x,'String','')
2554                set(handles.Coord_y,'String','')
2555            end
2556            Coord_z=get(handles.Coord_z,'String');
2557            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))REFRESH
2558                FieldList={};
2559                set(handles.Coord_z,'String','')
2560            end
2561        end
2562    else
2563        set(handles.FieldName,'Visible','off')
2564        set(handles.Field_text,'Visible','off')
2565    end
2566   
2567    set(handles_coord,'Visible','on')
2568    if isempty(find(strcmp('add_field...',FieldList)))
2569        FieldList=[FieldList;{'add_field...'}];%add 'add_field...' to the menu FieldName if it is not already
2570    end
2571    if FieldNameRequest_1 && numel(iview_netcdf)>=2
2572        set(handles.FieldName_1,'Visible','on')
2573        if CheckList_1==0        % not civ input made
2574            ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2575            ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2576            for ilist=1:numel(ind_var)
2577                if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2578                    FieldList_1={}; % previous choice not consistent with new input field
2579                    set(handles.FieldName_1,'Value',1)
2580                    break
2581                end
2582            end
2583            warn_coord=0;
2584            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2585                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2586                warn_coord=1;
2587            end
2588            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2589                FieldList_1={};
2590                warn_coord=1;
2591            end
2592            if warn_coord
2593                msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file')
2594            end
2595           
2596            set(handles.FieldName_1,'Visible','on')
2597            set(handles.FieldName_1,'Value',1)
2598            set(handles.FieldName_1,'String',FieldList_1)
2599        end
2600    else
2601        set(handles.FieldName_1,'Visible','off')
2602    end
2603    if isempty(FieldList)
2604        set(handles.Field_text,'Visible','off')
2605        set(handles.FieldName,'Visible','off')
2606    else
2607        set(handles.Field_text,'Visible','on')
2608        set(handles.FieldName,'Visible','on')
2609        set(handles.FieldName,'String',FieldList)
2610    end
2611else
2612    set(handles.InputFields,'Visible','off')
2613end
2614
2615%% Introduce visibility of file overwrite option
2616if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
2617    set(handles.CheckOverwrite,'Visible','on')
2618else
2619    set(handles.CheckOverwrite,'Visible','off')
2620end
2621
2622%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2623if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2624    [tild,iview]=sort(Param.InputTable(:,2)); % subdirectories sorted in alphabetical order
2625    set(handles.InputTable,'Data',Param.InputTable(iview,:));
2626    MinIndex_i=get(handles.MinIndex_i,'Data');
2627    MinIndex_j=get(handles.MinIndex_j,'Data');
2628    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2629    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2630    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2631    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2632    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2633    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
2634    TimeTable=get(handles.TimeTable,'Data');
2635    if size(TimeTable,1)<size(Param.InputTable,1)%if the time table is not complete, copy the missing lines from the previous ones
2636        for iline=size(TimeTable,1)+1:size(Param.InputTable,1)
2637            TimeTable(iline,:)=TimeTable(iline-1,:);
2638        end
2639    end
2640    set(handles.TimeTable,'Data',TimeTable(iview,:));% sort the time tables
2641    PairString=get(handles.PairString,'Data');
2642    set(handles.PairString,'Data',PairString(iview,:));
2643end
2644
2645%% Impose the whole input file index range if requested
2646if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2647    MinIndex_i=get(handles.MinIndex_i,'Data');
2648    MinIndex_j=get(handles.MinIndex_j,'Data');
2649    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2650    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2651    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2652    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2653    set(handles.num_incr_i,'String','1')
2654    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2655    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2656    set(handles.num_incr_j,'String','1')
2657else  % check index ranges
2658    first_i=1;last_i=1;first_j=1;last_j=1;
2659    if isfield(Param.IndexRange,'first_i')
2660        first_i=Param.IndexRange.first_i;
2661        last_i=Param.IndexRange.last_i;
2662    end
2663    if isfield(Param.IndexRange,'first_j')
2664        first_j=Param.IndexRange.first_j;
2665        last_j=Param.IndexRange.last_j;
2666    end
2667    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2668            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end
2669end
2670
2671%% enable or desable j index visibility
2672status_j='on'; % default
2673if isfield(SeriesData,'j1_series') && isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)) % case of empty j indices
2674    status_j='off'; % no j index needed
2675elseif strcmp(get(handles.PairString,'Visible'),'on')
2676    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j')); % =0 for burst case, 1 otherwise
2677    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2678        status_j='off'; % no j index needed for bust case
2679    end
2680end
2681enable_j(handles,status_j) % no j index needed
2682if isfield(ParamOut,'j_index_1')&& isfield(ParamOut,'j_index_2')%strcmp(ParamOut.Desable_j_index,'on')
2683    %status_j='off';
2684    set(handles.num_first_j,'String',num2str(ParamOut.j_index_1))
2685    set(handles.num_last_j,'String',num2str(ParamOut.j_index_2))
2686    set(handles.num_first_j,'enable','off')
2687    set(handles.num_last_j,'enable','off')
2688    set(handles.num_incr_j,'visible','off')
2689else
2690    set(handles.num_first_j,'enable','on')
2691    set(handles.num_last_j,'enable','on')
2692    set(handles.num_incr_j,'visible',status_j)
2693end
2694
2695%% NbSlice visibility
2696if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2697    set(handles.num_NbSlice,'Visible','on')
2698    set(handles.NbSlice_title,'Visible','on')
2699else
2700    set(handles.num_NbSlice,'Visible','off')
2701    set(handles.NbSlice_title,'Visible','off')
2702end
2703if isfield(ParamOut,'NbSlice') && isnumeric(ParamOut.NbSlice)
2704    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2705    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2706else
2707    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2708end
2709
2710%% Visibility of FieldTransform menu
2711FieldTransformVisible='off';  %hidden by default
2712if isfield(ParamOut,'FieldTransform')
2713    if ~strcmp(ParamOut.FieldTransform,'off')
2714    FieldTransformVisible='on'; 
2715    end
2716    if iscell(ParamOut.FieldTransform)
2717        SeriesData.TransformList=ParamOut.FieldTransform;
2718    end
2719    TransformName_Callback([],[], handles)
2720end
2721set(handles.FieldTransform,'Visible',FieldTransformVisible)
2722if isfield(ParamOut,'TransformPath')% record the path of transform function requested for compilation
2723    set(handles.TransformPath,'UserData',ParamOut.TransformPath)
2724else
2725    set(handles.TransformPath,'UserData',[])
2726end
2727
2728%% Visibility of projection object
2729ProjObjectVisible='off';  %hidden by default
2730if isfield(ParamOut,'ProjObject')
2731    ProjObjectVisible=ParamOut.ProjObject;
2732end
2733set(handles.CheckObject,'Visible',ProjObjectVisible)
2734if ~get(handles.CheckObject,'Value')
2735    ProjObjectVisible='off';
2736end
2737set(handles.ProjObjectName,'Visible',ProjObjectVisible)
2738set(handles.DeleteObject,'Visible',ProjObjectVisible)
2739set(handles.ViewObject,'Visible',ProjObjectVisible)
2740set(handles.EditObject,'Visible',ProjObjectVisible)
2741
2742%% Visibility of mask input
2743MaskVisible='off';  %hidden by default
2744if isfield(ParamOut,'Mask')
2745    MaskVisible=ParamOut.Mask;
2746end
2747set(handles.CheckMask,'Visible',MaskVisible);
2748%% Setting of expected iteration time
2749if isfield(ParamOut,'CPUTime')
2750    set(handles.num_CPUTime,'String',num2str(ParamOut.CPUTime));
2751end
2752
2753%% definition of the path for the output files
2754InputTable=get(handles.InputTable,'Data');
2755[OutputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
2756[OutputPath,Experiment,ExperimentExt]=fileparts(OutputPath);
2757set(handles.Device,'String',[Device DeviceExt])
2758set(handles.Device,'Visible','on')
2759set(handles.Device_title,'Visible','on')
2760set(handles.Experiment,'String',[Experiment ExperimentExt])
2761set(handles.Experiment,'Visible','on')
2762set(handles.Experiment_title,'Visible','on')
2763set(handles.Experiment_title,'Visible','on')
2764set(handles.OutputPath,'Visible','on')
2765set(handles.OutputPathBrowse,'Visible','on')
2766   
2767%% definition of the subdirectory containing the output files
2768
2769if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
2770    OutputDirExt='.series'; % default
2771    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2772        OutputDirExt=ParamOut.OutputDirExt;
2773    end
2774    set(handles.OutputDirExt,'String',OutputDirExt)
2775end
2776OutputDirVisible='off';
2777OutputSubDirMode='auto'; % default
2778SubDirOut='';
2779if isfield(ParamOut,'OutputSubDirMode')
2780    OutputSubDirMode=ParamOut.OutputSubDirMode;
2781end
2782switch OutputSubDirMode
2783    case 'auto' % default
2784        OutputDirVisible='on';
2785        SubDir=InputTable(1:end,2); % set of subdirectories
2786        SubDirOut=SubDir{1};
2787        if numel(SubDir)>1
2788            for ilist=2:numel(SubDir)
2789                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2790            end
2791        end
2792    case 'one'
2793        OutputDirVisible='on';
2794        SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output  subdirectory
2795    case 'two'
2796        OutputDirVisible='on';   
2797        SubDir=InputTable(1:2,2); % set of subdirectories
2798        SubDirOut=SubDir{1};
2799        if numel(SubDir)>1
2800                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2801        end
2802    case 'last'
2803        OutputDirVisible='on';
2804        SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output  subdirectory
2805end
2806set(handles.OutputSubDir,'String',SubDirOut)
2807set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
2808set(handles.OutputDirExt,'Visible',OutputDirVisible)
2809set(handles.OutputSubDir,'Visible',OutputDirVisible)
2810% set(handles.OutputDir_title,'Visible',OutputDirVisible)
2811SeriesData.ActionName=ActionName; % record ActionName for next use
2812
2813
2814%% visibility of the run mode (local or background or cluster)
2815if strcmp(OutputSubDirMode,'none')
2816    RunModeVisible='off'; % only local mode available if no output file is produced
2817else
2818    RunModeVisible='on';
2819end
2820set(handles.RunMode,'Visible',RunModeVisible)
2821set(handles.ActionExt,'Visible',RunModeVisible)
2822set(handles.RunMode_title,'Visible',RunModeVisible)
2823set(handles.ActionExt_title,'Visible',RunModeVisible)
2824
2825
2826%% Expected nbre of output files
2827if isfield(ParamOut,'OutputFileMode')
2828    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2829    set(handles.status,'UserData',StatusData)
2830end
2831
2832%% definition of an additional parameter set, determined by an ancillary GUI
2833if isfield(ParamOut,'ActionInput')
2834%     set(handles.ActionInput,'Visible','on')
2835    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2836    SeriesData.ActionInput=ParamOut.ActionInput;
2837else
2838%     set(handles.ActionInput,'Visible','off')
2839    if isfield(SeriesData,'ActionInput')
2840        SeriesData=rmfield(SeriesData,'ActionInput');
2841    end
2842end
2843set(handles.series,'UserData',SeriesData)
2844set(handles.ActionInput,'BackgroundColor',[1 0 0])
2845
2846
2847%------------------------------------------------------------------------
2848% --- Executes on button press in RefreshField.
2849function RefreshField_Callback(hObject, eventdata, handles)
2850%------------------------------------------------------------------------
2851set(handles.FieldName,'String',{'add_field...'});
2852set(handles.FieldName,'Value',1);
2853FieldName_Callback(hObject, eventdata, handles)
2854
2855
2856%------------------------------------------------------------------------
2857% --- Executes on selection change in FieldName.
2858function FieldName_Callback(hObject, eventdata, handles)
2859%------------------------------------------------------------------------
2860FieldListInit=get(handles.FieldName,'String');
2861field_index=get(handles.FieldName,'Value');
2862field=FieldListInit{field_index(1)};
2863if isequal(field,'add_field...')
2864    FieldListInit(field_index(1))=[];
2865    SeriesData=get(handles.series,'UserData');
2866    % input line for which the field choice is relevant
2867    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
2868    hget_field=findobj(allchild(0),'name','get_field');
2869    if ~isempty(hget_field)
2870        delete(hget_field)%delete opened versions of get_field
2871    end
2872    Param=read_GUI(handles.series);
2873    InputTable=Param.InputTable(iview,:);
2874    % check the existence of the first file in the series
2875    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1; % default setting for index j
2876    if isfield(Param.IndexRange,'first_j') % if index j is used     
2877        first_j=Param.IndexRange.first_j;
2878        last_j=Param.IndexRange.last_j;
2879        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2880        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2881    end
2882    PairString='';
2883    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2884    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2885    LineIndex=iview(1);
2886    if numel(iview)>1     
2887        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2888        LineIndex=str2num(answer);
2889    end
2890    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2891        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
2892    if exist(FirstFileName,'file') || ~isempty(regexp(InputTable{LineIndex,1},'^http'))
2893        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2894        ParamIn.SeriesInput=1;
2895        GetFieldData=get_field(FirstFileName,ParamIn);
2896        FieldList={};
2897        if isfield(GetFieldData,'FieldOption')% if a field has been selected
2898        switch GetFieldData.FieldOption
2899            case 'vectors'
2900                UName=GetFieldData.PanelVectors.vector_x;
2901                VName=GetFieldData.PanelVectors.vector_y;
2902                YName={GetFieldData.Coordinates.Coord_y};
2903                FieldList={['vec(' UName ',' VName ')'];...
2904                    ['norm(' UName ',' VName ')'];...
2905                    UName;VName};
2906                set(handles.VelType,'Visible','off')
2907            case {'scalar'}
2908                FieldList=GetFieldData.PanelScalar.scalar;
2909                YName={GetFieldData.Coordinates.Coord_y};
2910                if ischar(FieldList)
2911                    FieldList={FieldList};
2912                end
2913                set(handles.VelType,'Visible','off')
2914            case 'civdata...'
2915                FieldList=[set_field_list('U','V') ;{'C'}];
2916                set(handles.FieldName,'Value',1) % set menu to 'velocity
2917                XName='X';
2918                YName='y';
2919                set(handles.VelType,'Visible','on')
2920        end
2921        set(handles.FieldName,'Value',1)
2922        set(handles.FieldName,'String',[FieldListInit; FieldList; {'add_field...'}]);
2923        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2924           if ~isempty(regexp(FieldList{1},'^vec'))
2925                set(handles.FieldName,'Value',1)
2926           else
2927                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2928           end
2929            XName=GetFieldData.Coordinates.Coord_x;
2930            YName=GetFieldData.Coordinates.Coord_y;
2931            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2932            % get the time info                     
2933            TimeTable=get(handles.TimeTable,'Data');
2934            switch TimeNameStr
2935                case 'file index'
2936                    TimeName='';
2937                case 'attribute'
2938                    TimeName=['att:' GetFieldData.Time.TimeName];
2939                    % update the time table
2940                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
2941                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time             
2942                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
2943                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2944                case 'variable'
2945                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2946                    set(handles.NomType,'String','*')
2947                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2948                    set(handles.FileIndex,'String','')
2949                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2950                case 'matrix_index'
2951                    TimeName=['dim:' GetFieldData.Time.TimeName];
2952                    set(handles.NomType,'String','*')
2953                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2954                    set(handles.FileIndex,'String','')
2955                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2956            end
2957            TimeTable{LineIndex,1}=TimeName;
2958            set(handles.TimeTable,'Data',TimeTable);
2959        end
2960        set(handles.Coord_x,'String',XName)
2961        set(handles.Coord_y,'String',YName)
2962        set(handles.Coord_x,'Visible','on')
2963        set(handles.Coord_y,'Visible','on')
2964        end
2965    else
2966        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2967    end
2968end
2969
2970
2971function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2972[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2973FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2974Data=nc2struct(FileName,[]);
2975TimeValue=[];
2976DtValue=[];
2977if isequal(FileInfo.FileType,'civdata')
2978    if ismember(TimeName,{'civ1','filter1'})
2979        if isfield(Data,'Civ1_Time')
2980        TimeValue=Data.Civ1_Time;
2981        end
2982        if isfield(Data,'Civ1_Dt')
2983        DtValue=Data.Civ1_Dt;
2984        end
2985    else
2986        if isfield(Data,'Civ2_Time')
2987        TimeValue=Data.Civ2_Time;
2988        end
2989        if isfield(Data,'Civ2_Dt')
2990        DtValue=Data.Civ2_Dt;
2991        end
2992    end
2993else
2994    if ~isempty(TimeName)&& isfield(Data,TimeName)
2995        TimeValue=Data.(TimeName);
2996    end
2997    if exist('DtName','var') && isfield(Data,DtName)
2998        DtValue=Data.(DtName);
2999    end
3000end
3001
3002%------------------------------------------------------------------------
3003% --- Executes on selection change in FieldName_1.
3004function FieldName_1_Callback(hObject, eventdata, handles)
3005%------------------------------------------------------------------------
3006field_str=get(handles.FieldName_1,'String');
3007field_index=get(handles.FieldName_1,'Value');
3008field=field_str{field_index(1)};
3009if isequal(field,'add_field...')
3010    hget_field=findobj(allchild(0),'name','get_field');
3011    if ~isempty(hget_field)
3012        delete(hget_field)%delete opened versions of get_field
3013    end
3014    Param=read_GUI(handles.series);
3015    Param.InputTable=Param.InputTable(1,:);
3016    % check the existence of the first file in the series
3017    first_j=[];
3018    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
3019    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
3020    PairString='';
3021    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
3022    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
3023    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
3024        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
3025    if exist(FirstFileName,'file')
3026        ParamIn.SeriesInput=1;
3027        GetFieldData=get_field(FirstFileName,ParamIn);
3028        FieldList={};
3029        switch GetFieldData.FieldOption
3030            case 'vectors'
3031                UName=GetFieldData.PanelVectors.vector_x;
3032                VName=GetFieldData.PanelVectors.vector_y;
3033                FieldList={['vec(' UName ',' VName ')'];...
3034                    ['norm(' UName ',' VName ')'];...
3035                    UName;VName};
3036            case {'scalar','pick variables'}
3037                FieldList=GetFieldData.PanelScalar.scalar;
3038                if ischar(FieldList)
3039                    FieldList={FieldList};
3040                end
3041            case '1D plot'
3042
3043            case 'civdata...'
3044                FieldList=set_field_list('U','V','C');
3045                set(handles.FieldName,'Value',2) % set menu to 'velocity
3046        end
3047        if ~strcmp(GetFieldData.FieldOption,'civdata...')
3048            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
3049            switch TimeNameStr
3050                case 'file index'
3051                    set(handles.TimeName,'String','');
3052                case 'attribute'
3053                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
3054                case 'variable'
3055                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
3056                    set(handles.NomType,'String','*')
3057                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
3058                    set(handles.FileIndex,'String','')
3059                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
3060                case 'matrix_index'
3061                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
3062                    set(handles.NomType,'String','*')
3063                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
3064                    set(handles.FileIndex,'String','')
3065                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
3066            end
3067        end
3068        set(handles.FieldName_1,'Value',1)
3069        set(handles.FieldName_1,'String',[FieldList; {'add_field...'}]);
3070    end
3071end   
3072
3073
3074%%%%%%%%%%%%%
3075function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
3076indsel=ind_i;
3077indiff=diff(ind_i); % test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
3078indiff=[1 indiff last_i-ind_i(end)+1]; % for testing gaps with the imposed bounds
3079if ~isempty(indiff)
3080    indiff2=diff(indiff);
3081    indiffp=[indiff2 1];
3082    indiffm=[1 indiff2];
3083    ind_multi_m=find((indiff==0)&(indiffm<0))-1; % indices of first members of multiplets
3084    ind_multi_p=find((indiff==0)&(indiffp>0)); % indices of last members of multiplets
3085    %for each multiplet, select the most recent file
3086    ind_remove=[];
3087    for i=1:length(ind_multi_m)
3088        ind_pairs=ind_multi_m(i):ind_multi_p(i);
3089        for imulti=1:length(ind_pairs)
3090            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
3091        end
3092        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
3093        ind_s=indsort2(1:end-1); %
3094        ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
3095    end
3096end
3097
3098%------------------------------------------------------------------------
3099% --- determine the list of index pairstring of processing file
3100function [num_i1,num_i2,num_j1,num_j2,num_i_out,num_j_out]=find_file_indices(num_i,num_j,ind_shift,NomType,mode)
3101%------------------------------------------------------------------------
3102num_i1=num_i; % set of first image numbers by default
3103num_i2=num_i;
3104num_j1=num_j;
3105num_j2=num_j;
3106num_i_out=num_i;
3107num_j_out=num_j;
3108% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
3109if isequal(mode,'series(Di)')
3110    num_i1_line=num_i+ind_shift(3); % set of first image numbers
3111    num_i2_line=num_i+ind_shift(4);
3112    % adjust the first and last field number
3113        indsel=find(num_i1_line >= 1);
3114    num_i_out=num_i(indsel);
3115    num_i1_line=num_i1_line(indsel);
3116    num_i2_line=num_i2_line(indsel);
3117    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
3118    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
3119    [xx,num_i1]=meshgrid(num_j,num_i1_line);
3120    [xx,num_i2]=meshgrid(num_j,num_i2_line);
3121elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
3122    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
3123        num_j1=ind_shift(1)*ones(size(num_i));
3124        num_j2=ind_shift(2)*ones(size(num_i));
3125    else
3126        num_j1_col=num_j+ind_shift(1); % set of first image numbers
3127        num_j2_col=num_j+ind_shift(2);
3128        % adjust the first field number
3129        indsel=find((num_j1_col >= 1));   
3130        num_j_out=num_j(indsel);
3131        num_j1_col=num_j1_col(indsel);
3132        num_j2_col=num_j2_col(indsel);
3133        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
3134        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
3135    end   
3136end
3137
3138%------------------------------------------------------------------------
3139% --- Executes on button press in CheckObject.
3140function CheckObject_Callback(hObject, eventdata, handles)
3141%------------------------------------------------------------------------
3142hset_object=findobj(allchild(0),'tag','set_object'); % find the set_object interface handle
3143if get(handles.CheckObject,'Value')
3144    SeriesData=get(handles.series,'UserData');
3145    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)
3146        set(handles.ViewObject,'Value',1)
3147        ViewObject_Callback(hObject, eventdata, handles)
3148    else
3149        if ishandle(hset_object)
3150            uistack(hset_object,'top')% show the GUI set_object if opened
3151        else
3152            %get the object file
3153            InputTable=get(handles.InputTable,'Data');
3154            defaultname=InputTable{1,1};
3155            if isempty(defaultname)
3156                defaultname={''};
3157            end
3158            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
3159            if isempty(fileinput)% exit if no object file is selected
3160                set(handles.CheckObject,'Value',0)
3161                return
3162            end
3163            %read the file
3164            data=xml2struct(fileinput);
3165            if ~isfield(data,'Type')
3166                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
3167                set(handles.CheckObject,'Value',0)
3168                return
3169            end
3170            if ~isfield(data,'ProjMode')
3171                data.ProjMode='none';
3172            end
3173            hset_object=set_object(data); % call the set_object interface
3174            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
3175        end
3176        ProjObject=read_GUI(hset_object);
3177        set(handles.ProjObjectName,'String',ProjObject.Name); % display the object name
3178        SeriesData=get(handles.series,'UserData');
3179        SeriesData.ProjObject=ProjObject;
3180        set(handles.series,'UserData',SeriesData);
3181    end
3182    set(handles.EditObject,'Visible','on');
3183    set(handles.DeleteObject,'Visible','on');
3184    set(handles.ViewObject,'Visible','on');
3185    set(handles.ProjObjectName,'Visible','on');
3186else
3187    set(handles.EditObject,'Visible','off');
3188    set(handles.DeleteObject,'Visible','off');
3189    set(handles.ViewObject,'Visible','off');
3190    if ~ishandle(hset_object)
3191        set(handles.ViewObject,'Value',0);
3192    end
3193    set(handles.ProjObjectName,'Visible','off');
3194end
3195
3196%------------------------------------------------------------------------
3197% --- Executes on button press in ViewObject.
3198%------------------------------------------------------------------------
3199function ViewObject_Callback(hObject, eventdata, handles)
3200
3201UserData=get(handles.series,'UserData');
3202hset_object=findobj(allchild(0),'Tag','set_object');
3203if ~isempty(hset_object)
3204    delete(hset_object)% refresh set_object if already opened
3205end
3206hset_object=set_object(UserData.ProjObject);
3207set(hset_object,'Name','view_object_series')
3208
3209
3210%------------------------------------------------------------------------
3211% --- Executes on button press in EditObject.
3212function EditObject_Callback(hObject, eventdata, handles)
3213%------------------------------------------------------------------------
3214if get(handles.EditObject,'Value')
3215    set(handles.ViewObject,'Value',0)
3216    UserData=get(handles.series,'UserData');
3217    hset_object=set_object(UserData.ProjObject);
3218    set(hset_object,'Name','edit_object_series')
3219    set(get(hset_object,'Children'),'Enable','on')
3220else
3221    hset_object=findobj(allchild(0),'Tag','set_object');
3222    if ~isempty(hset_object)
3223        set(get(hset_object,'Children'),'Enable','off')
3224    end
3225end
3226
3227%------------------------------------------------------------------------
3228% --- Executes on button press in DeleteObject.
3229function DeleteObject_Callback(hObject, eventdata, handles)
3230%------------------------------------------------------------------------
3231SeriesData=get(handles.series,'UserData');
3232SeriesData.ProjObject=[];
3233set(handles.series,'UserData',SeriesData)
3234set(handles.ProjObjectName,'String','')
3235set(handles.ProjObjectName,'Visible','off')
3236set(handles.CheckObject,'Value',0)
3237set(handles.ViewObject,'Visible','off')
3238set(handles.EditObject,'Visible','off')
3239hset_object=findobj(allchild(0),'name','set_object_series');
3240if ~isempty(hset_object)
3241    delete(hset_object)
3242end
3243set(handles.DeleteObject,'Visible','off')
3244
3245%------------------------------------------------------------------------
3246% --- Executed when CheckMask is activated
3247%------------------------------------------------------------------------
3248function CheckMask_Callback(hObject, eventdata, handles)
3249
3250if get(handles.CheckMask,'Value')
3251    InputTable=get(handles.InputTable,'Data');
3252    nbview=size(InputTable,1);
3253    MaskTable=cell(nbview,1); % default
3254    ListMask=cell(nbview,1); % default
3255    MaskData=get(handles.MaskTable,'Data');
3256    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1); % complement if undefined lines
3257    for iview=1:nbview
3258        ListMask{iview,1}=num2str(iview);
3259        RootPath=InputTable{iview,1};
3260        if ~isempty(RootPath)
3261            if isempty(MaskData{iview})
3262                SubDir=InputTable{iview,2};
3263                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']); % take the root part of SubDir, before the first dot '.'
3264                if exist(MaskPath,'dir')
3265                    ListStruct=dir(MaskPath); % look for a mask file
3266                    ListCells=struct2cell(ListStruct); % transform dir struct to a cell arrray
3267                    check_dir=cell2mat(ListCells(4,:)); % =1 for directories, =0 for files
3268                    ListFiles=ListCells(1,:); % list of file and dri names
3269                    ListFiles=ListFiles(~check_dir); % list of file names (excluding dir)
3270                    mdetect=0;
3271                    if ~isempty(ListFiles)
3272                        for ifile=1:numel(ListFiles)
3273                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
3274                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
3275                                mdetect=1;
3276                                MaskName=ListFiles{ifile};
3277                            end
3278                            if ~strcmp(MaskFile{ifile},MaskFile{1})
3279                                mdetect=0; % cancel detection test in case of multiple masks, use the brower for selection
3280                                break
3281                            end
3282                        end
3283                    end
3284                    if mdetect==1
3285                        MaskName=fullfile(MaskPath,'mask_1.png');
3286                    else
3287                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
3288                    end
3289                else
3290                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3291                end
3292                MaskTable{iview,1}=MaskName ;
3293                ListMask{iview,1}=num2str(iview);
3294            end
3295        end
3296    end
3297    set(handles.MaskTable,'Data',MaskTable)
3298    set(handles.MaskTable,'Visible','on')
3299    set(handles.MaskBrowse,'Visible','on')
3300    set(handles.ListMask,'Visible','on')
3301    set(handles.ListMask,'String',ListMask)
3302    set(handles.ListMask,'Value',1)
3303else
3304    set(handles.MaskTable,'Visible','off')
3305    set(handles.MaskBrowse,'Visible','off')
3306    set(handles.ListMask,'Visible','off')
3307end
3308
3309%------------------------------------------------------------------------
3310% --- Executes on button press in MaskBrowse.
3311%------------------------------------------------------------------------
3312function MaskBrowse_Callback(hObject, eventdata, handles)
3313
3314InputTable=get(handles.InputTable,'Data');
3315iview=get(handles.ListMask,'Value');
3316RootPath=InputTable{iview,1};
3317MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3318if ~isempty(MaskName)
3319    MaskTable=get(handles.MaskTable,'Data');
3320    MaskTable{iview,1}=MaskName ;
3321    set(handles.MaskTable,'Data',MaskTable)
3322end
3323
3324%------------------------------------------------------------------------
3325% --- Executes when selected cell(s) is changed in MaskTable.
3326%------------------------------------------------------------------------
3327function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
3328
3329if numel(eventdata.Indices)>=1
3330set(handles.ListMask,'Value',eventdata.Indices(1))
3331end
3332
3333%-------------------------------------------------------------------
3334function MenuHelp_Callback(hObject, eventdata, handles)
3335%-------------------------------------------------------------------
3336
3337
3338% path_to_uvmat=which ('uvmat'); % check the path of uvmat
3339% pathelp=fileparts(path_to_uvmat);
3340% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3341% if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
3342% else
3343%     addpath (fullfile(pathelp,'uvmat_doc'))
3344%     web([helpfile '#series'])
3345% end
3346
3347%-------------------------------------------------------------------
3348% --- Executes on selection change in TransformName.
3349function TransformName_Callback(hObject, eventdata, handles)
3350%----------------------------------------------------------------------
3351TransformList=get(handles.TransformName,'String');
3352TransformIndex=get(handles.TransformName,'Value');
3353TransformName=TransformList{TransformIndex};
3354TransformPathList=get(handles.TransformName,'UserData');
3355nb_builtin_transform=4;
3356if isequal(TransformName,'more...');     
3357    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
3358    if isempty(FileName)
3359        return     %browser closed without choice
3360    end
3361    [TransformPath,TransformName,TransformExt]=fileparts(FileName); % removes extension .m
3362    if ~strcmp(TransformExt,'.m')
3363        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3364        return
3365    end
3366     % insert the choice in the menu
3367    TransformIndex=find(strcmp(TransformName,TransformList),1); % look for the selected function in the menu Action
3368    if isempty(TransformIndex)%the input string does not exist in the menu
3369        TransformIndex= length(TransformList);
3370        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)]; % the selected function is appended in the menu, before the last item 'more...'
3371        set(handles.TransformName,'String',TransformList)
3372        TransformPathList=[TransformPathList;{TransformPath}];
3373    else% the input function already exist, we update its path (possibly new)
3374        TransformPathList{TransformIndex}=TransformPath; %
3375        set(handles.TransformName,'Value',TransformIndex)
3376    end
3377   % save the new menu in the personal file 'uvmat_perso.mat'
3378   dir_perso=prefdir; % personal Matalb directory
3379   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3380   if exist(profil_perso,'file')
3381       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3382           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3383           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3384       end
3385       TransformPathListUser=TransformPathListUser';
3386       TransformListUser=TransformListUser';
3387       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); % store the root name for future opening of uvmat
3388   end
3389end
3390
3391%display the current function path
3392set(handles.TransformPath,'String',TransformPathList{TransformIndex}); % show the path to the senlected function
3393set(handles.TransformName,'UserData',TransformPathList);
3394
3395%% create the function handle of the selected fct
3396if ~isempty(TransformName)
3397    if ~exist(TransformPathList{TransformIndex},'dir')
3398        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3399        return
3400    end
3401    current_dir=pwd; % current working dir
3402    cd(TransformPathList{TransformIndex})
3403    transform_handle=str2func(TransformName);
3404    cd(current_dir)
3405    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3406    SeriesData=get(handles.series,'UserData');
3407    ParamIn=[];
3408    if isfield(SeriesData,'TransformInput')
3409        ParamIn.TransformInput=SeriesData.TransformInput;
3410    end
3411    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get the required conditions
3412    Field.Action.RUN=0; % indicate that the transform fct is called only to get input param
3413    %DataOut=feval(transform_handle,Field,[]); % execute the transform fct to get the required conditions
3414    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3415        SeriesData.TransformInput=DataOut.TransformInput;
3416        set(handles.series,'UserData',SeriesData)
3417    end
3418end
3419
3420%------------------------------------------------------------------------
3421% --- fct activated by the upper bar menu ExportConfig
3422%------------------------------------------------------------------------
3423function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3424
3425global Param
3426Param=read_GUI_series(handles);
3427evalin('base','global Param')%make CurData global in the workspace
3428display('current series config :')
3429evalin('base','Param') %display CurData in the workspace
3430commandwindow; % brings the Matlab command window to the front
3431
3432%------------------------------------------------------------------------
3433% --- fct activated by the upper bar menu InportConfig: import
3434%     menu settings from an xml file (stored in /0_XML for each run)
3435%------------------------------------------------------------------------
3436function MenuImportConfig_Callback(hObject, eventdata, handles)
3437
3438%% use a browser to choose the xml file containing the processing config
3439InputTable=get(handles.InputTable,'Data');
3440oldfile=InputTable{1,1}; % current path in InputTable
3441if isempty(oldfile)
3442    % use a file name stored in prefdir
3443    dir_perso=prefdir;
3444    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3445    if exist(profil_perso,'file')
3446        h=load (profil_perso);
3447        if isfield(h,'RootPath') && ischar(h.RootPath)
3448            oldfile=h.RootPath;
3449        end
3450    end
3451end
3452filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml'); % get the xml file containing processing parameters
3453if isempty(filexml), return, end % quit function if an xml file has not been opened
3454
3455%% fill the GUI series with the content of the xml file
3456[Param,RootTag,errormsg]=xml2struct(filexml); % read the input xml file as a Matlab structure
3457if ~isempty(errormsg)
3458    msgbox_uvmat('ERROR',errormsg);
3459    return
3460end
3461% ask to stop current Action if button RUN is in action (another process is already running)
3462if isequal(get(handles.RUN,'Value'),1)
3463    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3464    if strcmp(answer,'Yes')
3465        STOP_Callback(hObject, eventdata, handles)
3466    else
3467        return
3468    end
3469end
3470Param.Action.RUN=0; % desactivate the input RUN=1
3471
3472fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3473SeriesData=get(handles.series,'UserData');
3474if isfield(Param,'InputFields')
3475    ListField=Param.InputFields.FieldName;
3476    if ischar(ListField),ListField={ListField}; end
3477    set(handles.FieldName,'String',[ListField;{'add_field...'}])
3478     set(handles.FieldName,'Value',1:numel(ListField))
3479     set(handles.FieldName,'Visible','on')
3480end       
3481if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
3482%     set(handles.ActionInput,'Visible','on')
3483%     set(handles.ActionInput,'Value',0)
3484    Param.ActionInput.ConfigSource=filexml; % record the source of config for future info
3485    SeriesData.ActionInput=Param.ActionInput;
3486end
3487if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3488    SeriesData.TransformInput=Param.TransformInput;
3489end
3490if isfield(Param,'ProjObject') %introduce projection object if relevant
3491    SeriesData.ProjObject=Param.ProjObject;
3492end
3493set(handles.series,'UserData',SeriesData)
3494if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
3495    set(handles.ProjObjectName,'String',Param.ProjObject.Name)
3496    set(handles.ViewObject,'Visible','on')
3497    set(handles.EditObject,'Visible','on')
3498    set(handles.DeleteObject,'Visible','on')
3499else     
3500    set(handles.ProjObjectName,'String','')
3501    set(handles.ProjObjectName,'Visible','off')
3502    set(handles.ViewObject,'Visible','off')
3503    set(handles.EditObject,'Visible','off')
3504    set(handles.DeleteObject,'Visible','off')     
3505end     
3506set(handles.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated
3507
3508
3509%------------------------------------------------------------------------
3510% --- Executes when the GUI series is resized.
3511%------------------------------------------------------------------------
3512function series_ResizeFcn(hObject, eventdata, handles)
3513
3514%% input table
3515set(handles.InputTable,'Unit','pixel')
3516Pos=get(handles.InputTable,'Position');
3517set(handles.InputTable,'Unit','normalized')
3518ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3519ColumnWidth=num2cell(ColumnWidth);
3520set(handles.InputTable,'ColumnWidth',ColumnWidth)
3521
3522%% MinIndex_j and MaxIndex_i
3523unit=get(handles.MinIndex_i,'Unit');
3524set(handles.MinIndex_i,'Unit','pixel')
3525Pos=get(handles.MinIndex_i,'Position');
3526set(handles.MinIndex_i,'Unit',unit)
3527set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3528set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3529set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3530set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3531
3532%% TimeTable
3533set(handles.TimeTable,'Unit','pixel')
3534Pos=get(handles.TimeTable,'Position');
3535set(handles.TimeTable,'Unit','normalized')
3536% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3537ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3538set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3539
3540
3541%% PairString
3542set(handles.PairString,'Unit','pixel')
3543Pos=get(handles.PairString,'Position');
3544set(handles.PairString,'Unit','normalized')
3545set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3546
3547%% MaskTable
3548set(handles.MaskTable,'Unit','pixel')
3549Pos=get(handles.MaskTable,'Position');
3550set(handles.MaskTable,'Unit','normalized')
3551set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3552
3553%------------------------------------------------------------------------
3554% --- Executes on button press in status.
3555%------------------------------------------------------------------------
3556function status_Callback(hObject, eventdata, handles)
3557
3558if get(handles.status,'Value')
3559    set(handles.status,'BackgroundColor',[1 1 0])
3560    drawnow
3561    Param=read_GUI(handles.series);
3562    RootPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
3563    if ~isfield(Param,'OutputSubDir')   
3564        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3565        set(handles.status,'BackgroundColor',[0 1 0])
3566        return
3567    end
3568    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; % subdirectory for output files
3569    OutputDir=fullfile(RootPath,OutputSubDir);
3570    if exist(OutputDir,'dir')
3571        uigetfile_uvmat('status_display',OutputDir)
3572    else
3573        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3574        set(handles.status,'BackgroundColor',[0 1 0])
3575    end
3576else
3577    %% delete current display fig if selection is off
3578    set(handles.status,'BackgroundColor',[0 1 0])
3579    hfig=findobj(allchild(0),'name','status_display');
3580    if ~isempty(hfig)
3581        delete(hfig)
3582    end
3583    return
3584end
3585
3586
3587%------------------------------------------------------------------------   
3588% launched by selecting a file on the list
3589%------------------------------------------------------------------------
3590function view_file(hObject, eventdata)
3591
3592list=get(hObject,'String');
3593index=get(hObject,'Value');
3594rootroot=get(hObject,'UserData');
3595selectname=list{index};
3596ind_dot=regexp(selectname,'\.\.\.');
3597if ~isempty(ind_dot)
3598    selectname=selectname(1:ind_dot-1);
3599end
3600FullSelectName=fullfile(rootroot,selectname);
3601if exist(FullSelectName,'dir')% a directory has been selected
3602    ListFiles=dir(FullSelectName);
3603    ListDisplay=cell(numel(ListFiles),1);
3604    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3605        ListDisplay{ilist-1}=ListFiles(ilist).name;
3606    end
3607    set(hObject,'Value',1)
3608    set(hObject,'String',ListDisplay)
3609    if strcmp(selectname,'..')
3610        FullSelectName=fileparts(fileparts(FullSelectName));
3611    end
3612    set(hObject,'UserData',FullSelectName)
3613    hfig=get(hObject,'parent');
3614    htitlebox=findobj(hfig,'tag','titlebox');   
3615    set(htitlebox,'String',FullSelectName)
3616elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3617    FileInfo=get_file_info(FullSelectName);   
3618    if strcmp(FileInfo.FileType,'txt')
3619        edit(FullSelectName)
3620    elseif strcmp(FileInfo.FileType,'xml')
3621        editxml(FullSelectName)
3622    else
3623        uvmat(FullSelectName)
3624    end
3625    set(gcbo,'Value',1)
3626end
3627
3628
3629%------------------------------------------------------------------------   
3630% launched by refreshing the status figure
3631%------------------------------------------------------------------------
3632function refresh_GUI(hfig)
3633
3634htitlebox=findobj(hfig,'tag','titlebox');
3635hlist=findobj(hfig,'tag','list');
3636hseries=findobj(allchild(0),'tag','series');
3637hstatus=findobj(hseries,'tag','status');
3638StatusData=get(hstatus,'UserData');
3639OutputDir=get(htitlebox,'String');
3640if ischar(OutputDir),OutputDir={OutputDir};end
3641ListFiles=dir(OutputDir{1});
3642if numel(ListFiles)<1
3643    return
3644end
3645ListFiles(1)=[]; % removes the first line ='.'
3646ListDisplay=cell(numel(ListFiles),1);
3647testrecent=0;
3648datnum=zeros(numel(ListDisplay),1);
3649for ilist=1:numel(ListDisplay)
3650    ListDisplay{ilist}=ListFiles(ilist).name;
3651      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3652            datnum(ilist)=ListFiles(ilist).datenum; % only available in recent matlab versions
3653            testrecent=1;
3654       end
3655end
3656set(hlist,'String',ListDisplay)
3657
3658%% Look at date of creation
3659ListDisplay=ListDisplay(datnum~=0);
3660datnum=datnum(datnum~=0); % keep the non zero values corresponding to existing files
3661NbOutputFile=[];
3662if isempty(datnum)
3663    if testrecent
3664        message='no civ result created yet';
3665    else
3666        message='';
3667    end
3668else
3669    [first,indfirst]=min(datnum);
3670    [last,indlast]=max(datnum);
3671    NbOutputFile_str='?';
3672    NbOutputFile=[];
3673    if isfield(StatusData,'NbOutputFile')
3674        NbOutputFile=StatusData.NbOutputFile;
3675        NbOutputFile_str=num2str(NbOutputFile);
3676    end
3677    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3678        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3679end
3680set(htitlebox,'String', [OutputDir{1};message])
3681
3682%% update the waitbar
3683hwaitbar=findobj(hfig,'tag','waitbar');
3684if ~isempty(NbOutputFile)
3685    BarPosition=get(hwaitbar,'Position');
3686    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3687    set(hwaitbar,'Position',BarPosition)
3688end
3689
3690%------------------------------------------------------------------------
3691% --- Executes on selection change in ActionExt.
3692%------------------------------------------------------------------------
3693function ActionExt_Callback(hObject, eventdata, handles)
3694
3695ActionExtList=get(handles.ActionExt,'String');
3696ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3697if strcmp(ActionExt,'.py (in dev.)')
3698    set(handles.RunMode,'Value',2)
3699end
3700
3701
3702function num_NbSlice_Callback(hObject, eventdata, handles)
3703NbSlice=str2num(get(handles.num_NbSlice,'String'));
3704
3705%------------------------------------------------------------------------
3706% --- set the visibility of relevant velocity type menus:
3707function menu=set_veltype_display(Civ,FileType)
3708%------------------------------------------------------------------------
3709if ~exist('FileType','var')
3710    FileType='civx';
3711end
3712switch FileType
3713    case 'civx'
3714        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3715        if isequal(Civ,0)
3716            imax=0;
3717        elseif isequal(Civ,1) || isequal(Civ,2)
3718            imax=1;
3719        elseif isequal(Civ,3)
3720            imax=3;
3721        elseif isequal(Civ,4) || isequal(Civ,5)
3722            imax=4;
3723        elseif isequal(Civ,6) %patch2
3724            imax=6;
3725        end
3726    case 'civdata'
3727        menu={'civ1';'filter1';'civ2';'filter2'};
3728        if isequal(Civ,0)
3729            imax=0;
3730        elseif isequal(Civ,1) || isequal(Civ,2)
3731            imax=1;
3732        elseif isequal(Civ,3)
3733            imax=2;
3734        elseif isequal(Civ,4) || isequal(Civ,5)
3735            imax=3;
3736        else%if isequal(Civ,6) %patch2
3737            imax=4;
3738        end
3739end
3740menu=menu(1:imax);
3741
3742
3743% --- Executes on mouse motion over figure - except title and menu.
3744% function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3745% set(hObject,'Pointer','arrow');
3746
3747
3748% --- Executes on button press in SetPairs.
3749function SetPairs_Callback(hObject, eventdata, handles)
3750
3751%% delete previous occurrence of 'set_pairs'
3752hfig=findobj(allchild(0),'Tag','set_pairs');
3753if ~isempty(hfig)
3754delete(hfig)
3755end
3756
3757%% create the GUI set_pairs
3758set(0,'Unit','points')
3759ScreenSize=get(0,'ScreenSize'); % get the size of the screen, to put the fig on the upper right
3760Width=220; % fig width in points (1/72 inch)
3761Height=min(0.8*ScreenSize(4),300);
3762Left=ScreenSize(3)- Width-40; % right edge close to the right, with margin=40
3763Bottom=ScreenSize(4)-Height-40; % put fig at top right
3764hfig=findobj(allchild(0),'Tag','set_slice');
3765if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI
3766hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3767BackgroundColor=get(hfig,'Color');
3768SeriesData=get(handles.series,'UserData');
3769TimeUnit=get(handles.TimeUnit,'String');
3770PairString=get(handles.PairString,'Data');
3771ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs
3772ListViewMenu=cell(numel(ListViewLines),1);
3773%iview=get(handles.PairString,'Value');
3774iview=[];
3775for ilist=1:numel(ListViewLines)
3776    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3777end
3778if isempty(iview)
3779    ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs
3780    iview=ListViewLines(end);
3781else
3782    ListViewValue=find(ListViewLines==iview);
3783end
3784ref_i=str2num(get(handles.num_first_i,'String'));
3785ref_j=1; % default
3786if strcmp(get(handles.num_first_j,'String'),'Visible')
3787    ref_j=str2num(get(handles.num_first_j,'String'));
3788end
3789[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j2_series{1});
3790InputTable=get(handles.InputTable,'Data');
3791displ_pair=update_listpair(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j1_series{1},SeriesData.j2_series{1},ModeMenu{ModeValue},...
3792                                                 SeriesData.Time{1},TimeUnit,ref_i,ref_j,SeriesData.TimeName,InputTable,SeriesData.FileInfo{1});
3793for iline=1:size(InputTable,1)
3794    viewcell{iline}=num2str(iline);
3795end
3796viewcell=viewcell';
3797ModeMenu={'bursts';'series(Dj)'};
3798ModeValue=1;                                               
3799                   %i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo                             
3800% first raw of the GUI
3801uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3802    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right'); % title
3803uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3804    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',viewcell,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3805    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3806% second raw of the GUI
3807uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3808    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3809uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3810    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3811    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3812% third raw
3813uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3814    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3815uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3816    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3817    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3818uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3819    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center'); % title
3820uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3821    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3822    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3823uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3824    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3825    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
3826uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3827    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3828    'Tag','OK','TooltipString','''OK'': validate the choice');
3829%  last raw  of the GUI: pushbuttons
3830% uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.35 0.01 0.3 0.15],'BackgroundColor',[0 1 0],'String','OK','Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),...
3831%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3832drawnow
3833
3834%------------------------------------------------------------------------
3835function ListView_Callback(hObject,eventdata)
3836Mode_Callback(hObject,eventdata)
3837
3838%------------------------------------------------------------------------   
3839function Mode_Callback(hObject,eventdata)
3840%% get input info
3841hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series
3842hhseries=guidata(hseries); % handles of the elements in the GUI series
3843TimeUnit=get(hhseries.TimeUnit,'String');
3844SeriesData=get(hseries,'UserData');
3845mode_list=get(hObject,'String');
3846mode=mode_list{get(hObject,'Value')};
3847hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3848iview=get(hListView,'Value');
3849i1_series=SeriesData.i1_series{iview};
3850i2_series=SeriesData.i2_series{iview};
3851j1_series=SeriesData.j1_series{iview};
3852j2_series=SeriesData.j2_series{iview};
3853
3854%% enable j index visibility after the new choice
3855
3856if strcmp(mode,'series(Dj)')
3857   status_j='on'; % default
3858else
3859       status_j='off'; % no j index needed for bust case
3860end
3861enable_j(hhseries,status_j) % no j index needed
3862
3863%% get the reference indices for the time interval Dt
3864href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3865ref_i=[];ref_j=[];
3866if strcmp(get(href_i,'Visible'),'on')
3867    ref_i=str2num(get(href_i,'String'));
3868end
3869if isempty(ref_i)
3870    ref_i=1;
3871end
3872if isempty(ref_j)
3873    ref_j=1;
3874end
3875
3876%% update the menu ListPair
3877Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo);
3878hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3879set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3880set(hlist_pairs,'String',Menu)% set the menu in ListPair
3881ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3882
3883%-------------------------------------------------------------
3884% --- Executes on selection in ListPair.
3885function ListPair_Callback(hObject,eventdata)
3886%------------------------------------------------------------
3887list_pair=get(hObject,'String'); % get the menu of image pairs
3888if isempty(list_pair)
3889    string='';
3890else
3891    string=list_pair{get(hObject,'Value')};
3892   % string=regexprep(string,',.*',''); % removes time indication (after ',')
3893end
3894hseries=findobj(allchild(0),'tag','series');
3895hPairString=findobj(hseries,'tag','PairString');
3896PairString=get(hPairString,'Data');
3897hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3898iview=get(hListView,'Value');
3899PairString{iview,1}=string;
3900% report the selected pair string to the table PairString
3901set(hPairString,'Data',PairString)
3902
3903
3904%------------------------------------------------------------------------
3905function num_ref_i_Callback(hObject, eventdata)
3906%------------------------------------------------------------------------
3907Mode_Callback([],[])
3908
3909%------------------------------------------------------------------------
3910function num_ref_j_Callback(hObject, eventdata)
3911%------------------------------------------------------------------------
3912Mode_Callback([],[])
3913
3914%------------------------------------------------------------------------
3915function OK_Callback(hObject, eventdata)
3916%------------------------------------------------------------------------
3917delete(get(hObject,'parent'))
3918
3919
3920%------------------------------------------------------------------------
3921% --- Executes on button press in ClearLine.
3922%------------------------------------------------------------------------
3923function ClearLine_Callback(hObject, eventdata, handles)
3924InputTable=get(handles.InputTable,'Data');
3925iline=str2double(get(handles.InputLine,'String'));
3926if size(InputTable,1)>1
3927    InputTable(iline,:)=[]; % suppress the current line if not the first
3928    set(handles.InputTable,'Data',InputTable);
3929end
3930set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
3931
3932
3933% --- Executes on button press in MonitorCluster.
3934function MonitorCluster_Callback(hObject, eventdata, handles)
3935
3936[rr,ss]=system('oarstat |grep N=UVmat');% check the list of jobs launched with uvmat
3937if isempty(ss)
3938   disp( 'no job presently submitted with uvmat')
3939else
3940    disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime')
3941    disp(ss)
3942end
3943
3944
3945function OutputSubDir_Callback(hObject, eventdata, handles)
3946set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
3947
3948
3949% --- Executes on button press in CheckOverwrite.
3950function CheckOverwrite_Callback(hObject, eventdata, handles)
3951
3952% --- Executes on button press in TestCPUTime.
3953function TestCPUTime_Callback(hObject, eventdata, handles)
3954% hObject    handle to TestCPUTime (see GCBO)
3955% eventdata  reserved - to be defined in a future version of MATLAB
3956% handles    structure with handles and user data (see GUIDATA)
3957
3958
3959% --- Executes on button press in DiskQuota.
3960function DiskQuota_Callback(hObject, eventdata, handles)
3961SeriesData=get(handles.series,'UserData');
3962system(SeriesData.SeriesParam.DiskQuotaCmd)
3963
3964
3965% --- Executes on button press in Replicate.
3966function Replicate_Callback(hObject, eventdata, handles)
3967if get(handles.Replicate,'Value')
3968    InputTable=get(handles.InputTable,'Data');
3969    for ilist=1:size(InputTable,1)
3970        InputDir{ilist}=fullfile(InputTable{ilist,1},InputTable{ilist,2});
3971    end
3972    browse_data(InputDir)
3973else
3974    hh=findobj(allchild(0),'Tag','browse_data');
3975    if ~isempty(hh)
3976        delete(hh)
3977    end
3978end
3979
3980
3981
3982
3983function OutputPath_Callback(hObject, eventdata, handles)
3984
3985
3986function Experiment_Callback(hObject, eventdata, handles)
3987
3988
3989function Device_Callback(hObject, eventdata, handles)
3990
3991
3992% --- Executes on button press in OutputPathBrowse.
3993function OutputPathBrowse_Callback(hObject, eventdata, handles)
3994CheckValue=get(handles.OutputPathBrowse,'Value');
3995if CheckValue
3996OutputPath=uigetdir(get(handles.OutputPath,'String'));
3997set(handles.OutputPath,'String',OutputPath)
3998else
3999    InputTable=get(handles.InputTable,'Data');
4000    set(handles.OutputPath,'String',InputTable{1,1})
4001end
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